Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A MONOVACCENIN LIPID CUBIC PHASE
 
Authors :  N. Hoefer, D. Aragao, M. Caffrey
Date :  08 Jun 11  (Deposition) - 18 Jul 12  (Release) - 18 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Antibiotic, Ion Channel, Mesophase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Hoefer, D. Aragao, M. Caffrey
Crystallization Of Gramicidin From A Monovaccenin Lipidic Cubic Phase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - VAL-GRAMICIDIN A
    Atcc: 8246
    Chains: A, B, C, D
    Organism Scientific: BREVIBACILLUS BREVIS
    Organism Taxid: 1393
    Synonym: GRAMICIDIN D

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 35)

Asymmetric/Biological Unit (5, 35)
No.NameCountTypeFull Name
1DLE16Mod. Amino AcidD-LEUCINE
2DVA8Mod. Amino AcidD-VALINE
3ETA4Mod. Amino AcidETHANOLAMINE
4FVA4Mod. Amino AcidN-FORMYL-L-VALINE
5MVC3Ligand/IonMONOVACCENIN

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDVA A:6 , TRP A:11 , DLE A:12 , DLE B:4 , TRP B:9 , FVA C:1 , TRP C:13 , HOH C:2002 , TRP D:9BINDING SITE FOR RESIDUE MVC C1016
2AC2SOFTWARETRP A:13 , TRP C:11 , DLE C:12 , DLE D:4 , TRP D:9BINDING SITE FOR RESIDUE MVC C1017
3AC3SOFTWARETRP A:15 , ETA A:16 , FVA B:1 , FVA C:1 , TRP C:15BINDING SITE FOR RESIDUE MVC C1018

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZQ8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZQ8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZQ8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZQ8)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZQ8)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  3zq8 A  1 xGAxAxVxWxWxWxWx 16
                            |  | | |10 | | |
                            |  | | | | | | |
                            1-FVA| | | | | |
                               4-DLE | | | |
                                 6-DVA | | |
                                   8-DVA | |
                                    10-DLE |
                                      12-DLE
                                        14-DLE
                                          16-ETA


Chain B from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  3zq8 B  1 xGAxAxVxWxWxWxWx 16
                            |  | | |10 | | |
                            |  | | | | | | |
                            1-FVA| | | | | |
                               4-DLE | | | |
                                 6-DVA | | |
                                   8-DVA | |
                                    10-DLE |
                                      12-DLE
                                        14-DLE
                                          16-ETA


Chain C from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  3zq8 C  1 xGAxAxVxWxWxWxWx 16
                            |  | | |10 | | |
                            |  | | | | | | |
                            1-FVA| | | | | |
                               4-DLE | | | |
                                 6-DVA | | |
                                   8-DVA | |
                                    10-DLE |
                                      12-DLE
                                        14-DLE
                                          16-ETA


Chain D from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  3zq8 D  1 xGAxAxVxWxWxWxWx 16
                            |  | | |10 | | |
                            |  | | | | | | |
                            1-FVA| | | | | |
                               4-DLE | | | |
                                 6-DVA | | |
                                   8-DVA | |
                                    10-DLE |
                                      12-DLE
                                        14-DLE
                                          16-ETA
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3ZQ8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZQ8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZQ8)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3ZQ8)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    DLE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DVA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ETA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FVA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MVC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3zq8)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3zq8
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 3ZQ8)

(-) Related Entries Specified in the PDB File

1al4 GRAMICIDIN D FROM BACILLUS BREVIS (N- PROPANOL SOLVATE)
1alx GRAMICIDIN D FROM BACILLUS BREVIS (METHANOL SOLVATE)
1alz GRAMICIDIN D FROM BACILLUS BREVIS (ETHANOL SOLVATE)
1av2 GRAMICIDIN A/CSCL COMPLEX, ACTIVE AS A DIMER
1bdw GRAMICIDIN D FROM BACILLUS BREVIS (ACTIVE FORM)
1c4d GRAMICIDIN CSCL COMPLEX
1gmk GRAMICIDIN/KSCN COMPLEX
1grm GRAMICIDIN A (NMR, 5 STRUCTURES)
1jno GRAMICIDIN A IN SODIUM DODECYL SULFATE MICELLES (NMR)
1jo3 GRAMICIDIN B IN SODIUM DODECYL SULFATE MICELLES (NMR)
1jo4 GRAMICIDIN C IN SODIUM DODECYL SULFATE MICELLES (NMR)
1kqe SOLUTION STRUCTURE OF A LINKED SHORTENED GRAMICIDIN A INBENZENE/ACETONE 10:1
1mag GRAMICIDIN A IN HYDRATED DMPC BILAYERS, SOLID STATE NMR
1mic GRAMICIDIN A: LEFT-HANDED PARALLEL DOUBLE HELICAL FORM IN METHANOL IN THE PRESENCE OF CACL2, NMR, 20 STRUCTURES
1ng8 G15-GRAMICIDIN A IN SODIUM DODECYL SULFATE MICELLES (NMR)
1nrm GRAMICIDIN A IN DODECYL PHOSPHOCHOLINE MICELLES (NMR)
1nru GRAMICIDIN A IN DODECYL PHOSPHOCHOLINE MICELLES IN THEPRESENCE OF EXCESS NA+ (NMR)
1nt5 F1-GRAMICIDIN A IN SODIUM DODECYL SULFATE MICELLES (NMR)
1nt6 F1-GRAMICIDIN C IN SODIUM DODECYL SULFATE MICELLES (NMR)
1tkq SOLUTION STRUCTURE OF A LINKED UNSYMMETRIC GRAMICIDIN IN AMEMBRANE-ISOELECTRICAL SOLVENTS MIXTURE IN THE PRESENCE OFCSCL
1w5u GRAMICIDIN D FROM BACILLUS BREVIS (ETHANOL SOLVATE)
2izq GRAMICIDIN D COMPLEX WITH KI
2xdc STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A LIPID CUBIC PHASE.
2y5m STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A 7.7 MONOACYLGLYCEROL LIPID CUBIC PHASE.
2y6n STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A 8.8 MONOACYLGLYCEROL LIPID CUBIC PHASE.