1M91 - JenaLib

Theoretical Model (Jmol Viewer)

Title :   A THEORETICAL MODEL OF NADH-CYTOCHROME B5 REDUCTASE (HUMAN)

Authors :   R. Ravulapalli, S. Muruganantham

Date :   26 Jul 02 (Deposition) - 14 Aug 02 (Release) - 14 Aug 02 (Revision)

Method :   THEORETICAL MODEL

Resolution :   NOT APPLICABLE

Chains :   Theor. Model : A

Keywords :   Oxidoreductase, Flavoprotein, Fad, Nad, Membrane, Myristate, Lipoprotein, Endoplasmic Reticulum, Disease Mutatio, Polymorphism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Ravulapalli, S. Muruganantham
A Theoretical Model Of Nadh-Cytochrome B5 Reductase (Human)
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - NADH-CYTOCHROME B5 REDUCTASE
	Chains	:	A
	EC Number	:	1.6.2.2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS


Theoretical Model	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1M91)

(no "Site" information available for 1M91)

(no "SS Bond" information available for 1M91)

Theoretical Model

No.	Residues
1	Gly A:143	-	Pro A:144

Theoretical Model (11, 11)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_004619	R	58	Q	NB5R3_HUMAN	Disease (METHB-CYB5R3)	121965007	A	R	57	Q
02	UniProt	VAR_018419	S	66	P	NB5R3_HUMAN	Polymorphism	1130706	A	S	65	P
03	UniProt	VAR_010750	L	73	P	NB5R3_HUMAN	Disease (METHB-CYB5R3)	121965013	A	L	72	P
04	UniProt	VAR_004620	V	106	M	NB5R3_HUMAN	Disease (METHB-CYB5R3)	121965009	A	V	105	M
05	UniProt	VAR_010751	T	117	S	NB5R3_HUMAN	Polymorphism	1800457	A	T	116	S
06	UniProt	VAR_004621	S	128	P	NB5R3_HUMAN	Disease (METHB-CYB5R3)	121965006	A	S	127	P
07	UniProt	VAR_004622	L	149	P	NB5R3_HUMAN	Disease (METHB-CYB5R3)	121965008	A	L	148	P
08	UniProt	VAR_010752	A	179	V	NB5R3_HUMAN	Disease (METHB-CYB5R3)	201232518	A	A	178	V
09	UniProt	VAR_010753	C	204	R	NB5R3_HUMAN	Disease (METHB-CYB5R3)	121965011	A	C	203	R
10	UniProt	VAR_010754	C	204	Y	NB5R3_HUMAN	Disease (METHB-CYB5R3)	121965015	A	C	203	Y
11	UniProt	VAR_037316	G	292	D	NB5R3_HUMAN	Disease (METHB-CYB5R3)	121965016	A	G	291	D

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Theoretical Model (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FAD_FR	PS51384	Ferredoxin reductase-type FAD binding domain profile.	NB5R3_HUMAN	40-152	1	A:39-151

Theoretical Model (9, 9)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000352397	1a	ENSE00001892790	chr22:43045574-43045301	274	NB5R3_HUMAN	1-7	7	1	A:1-6	6
1.3b	ENST00000352397	3b	ENSE00001651348	chr22:43032852-43032721	132	NB5R3_HUMAN	8-51	44	1	A:7-50	44
1.4b	ENST00000352397	4b	ENSE00000656632	chr22:43027456-43027384	73	NB5R3_HUMAN	52-76	25	1	A:51-75	25
1.4d	ENST00000352397	4d	ENSE00001785090	chr22:43026994-43026888	107	NB5R3_HUMAN	76-111	36	1	A:75-110	36
1.5	ENST00000352397	5	ENSE00001676775	chr22:43024287-43024158	130	NB5R3_HUMAN	112-155	44	1	A:111-154	44
1.6b	ENST00000352397	6b	ENSE00001804814	chr22:43023694-43023611	84	NB5R3_HUMAN	155-183	29	1	A:154-182	29
1.7	ENST00000352397	7	ENSE00001725986	chr22:43023395-43023310	86	NB5R3_HUMAN	183-211	29	1	A:182-210	29
1.8	ENST00000352397	8	ENSE00001695409	chr22:43019894-43019795	100	NB5R3_HUMAN	212-245	34	1	A:211-244	34
1.9f	ENST00000352397	9f	ENSE00000880579	chr22:43015951-43014814	1138	NB5R3_HUMAN	245-301	57	1	A:244-300	57

Theoretical Model

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:300
 aligned with NB5R3_HUMAN | P00387 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:300
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301
          NB5R3_HUMAN     2 GAQLSTLGHMVLFPVWFLYSLLMKLFQRSTPAITLESPDIKYPLRLIDREIISHDTRRFRFALPSPQHILGLPVGQHIYLSARIDGNLVVRPYTPISSDDDKGFVDLVIKVYFKDTHPKFPAGGKMSQYLESMQIGDTIEFRGPSGLLVYQGKGKFAIRPDKKSNPIIRTVKSVGMIAGGTGITPMLQVIRAIMKDPDDHTVCHLLFANQTEKDILLRPELEELRNKHSARFKLWYTLDRAPEAWDYGQGFVNEEMIRDHLPPPEEEPLVLMCGPPPMIQYACLPNLDHVGHPTERCFVF 301
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........................................eeeeeeeeee.....eeeeee..............eeeeeeee..eeeeeee..........eeeee...............hhhhhhhhhh....eeeeeeee..eeeee..eeee........eeee..eeeeeee..hhhhhhhhhhhhhhh.....eeeeeeee.hhhhh..hhhhhhhhhhhh..eeeeeee.........ee...hhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhh.hhh.eee. Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------------------------Q-------P------P--------------------------------M----------S----------P--------------------P-----------------------------V------------------------R---------------------------------------------------------------------------------------D--------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE --------------------------------------FAD_FR  PDB: A:39-151 UniProt: 40-152                                                                            ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1a  Exon 1.3b  PDB: A:7-50 UniProt: 8-51        Exon 1.4b  PDB: A:51-75  -----------------------------------Exon 1.5  PDB: A:111-154 UniProt: 112-155   ---------------------------Exon 1.7  PDB: A:182-210     Exon 1.8  PDB: A:211-244          -------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------Exon 1.4d  PDB: A:75-110            -------------------------------------------Exon 1.6b  PDB: A:154-182    -------------------------------------------------------------Exon 1.9f  PDB: A:244-300 UniProt: 245-301                Transcript 1 (2)
                 1m91 A   1 GAQLSTLGHMVLFPVWFLYSLLMKLFQRSTPAITLESPDIKYPLRLIDREIISHDTRRFRFALPSPQHILGLPVGQHIYLSARIDGNLVVRPYTPISSDDDKGFVDLVIKVYFKDTHPKFPAGGKMSQYLESMQIGDTIEFRGPSGLLVYQGKGKFAIRPDKKSNPIIRTVKSVGMIAGGTGITPMLQVIRAIMKDPDDHTVCHLLFANQTEKDILLRPELEELRNKHSARFKLWYTLDRAPEAWDYGQGFVNEEMIRDHLPPPEEEPLVLMCGPPPMIQYACLPNLDHVGHPTERCFVF 300
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 1M91)

(no "CATH Domain" information available for 1M91)

(no "Pfam Domain" information available for 1M91)

Theoretical Model(hide GO term definitions)

Chain A (NB5R3_HUMAN | P00387)

molecular function
	GO:0043531	ADP binding	Interacting selectively and non-covalently with ADP, adenosine 5'-diphosphate.
	GO:0016208	AMP binding	Interacting selectively and non-covalently with AMP, adenosine monophosphate.
	GO:0071949	FAD binding	Interacting selectively and non-covalently with the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	GO:0004128	cytochrome-b5 reductase activity, acting on NAD(P)H	Catalysis of the reaction: NAD(P)H + H+ + 2 ferricytochrome b(5) = NAD(P)+ + 2 ferrocytochrome b(5).
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0019852	L-ascorbic acid metabolic process	The chemical reactions and pathways involving L-ascorbic acid, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate; L-ascorbic acid is vitamin C and has co-factor and anti-oxidant activities in many species.
	GO:0008015	blood circulation	The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products.
	GO:0006695	cholesterol biosynthetic process	The chemical reactions and pathways resulting in the formation of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
	GO:0008203	cholesterol metabolic process	The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006694	steroid biosynthetic process	The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
	GO:0008202	steroid metabolic process	The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
	GO:0016126	sterol biosynthetic process	The chemical reactions and pathways resulting in the formation of sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005833	hemoglobin complex	An iron-containing, oxygen carrying complex. In vertebrates it is made up of two pairs of associated globin polypeptide chains, each chain carrying a noncovalently bound heme prosthetic group.
	GO:0005811	lipid droplet	An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005743	mitochondrial inner membrane	The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
	GO:0005741	mitochondrial outer membrane	The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Theoretical Model
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1m91)

	Sites
(no "Sites" information available for 1m91)

	Cis Peptide Bonds
		Gly A:143 - Pro A:144	[ RasMol ]

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	1m91
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	NB5R3_HUMAN \| P00387
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	1.6.2.2
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	250800
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UniProtKB/Swiss-Prot
	NB5R3_HUMAN \| P00387	:	1umk

1i7p	1I7P CONTAINS RAT B5R IN COMPLEX WITH FAD
1ndh	1NDH CONTAINS NADH-CYTOCHROME B5 REDUCTASE FROM PIG LIVER AT 2.4 A RESOLUTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (11, 11)

PROSITE Motifs (1, 1)

Exons (9, 9)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (26, 26)

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