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(-) Description

Title :  CRYSTAL STRUCTURE OF A CHEMICALLY SYNTHESIZED [D25N]HIV-1 PROTEASE MOLECULE COMPLEXED WITH MVT-101 REDUCED ISOSTERE INHIBITOR
 
Authors :  V. Y. Torbeev, S. B. H. Kent
Date :  13 Jul 09  (Deposition) - 27 Jul 11  (Release) - 27 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Beta-Sheet, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Y. Torbeev, S. B. H. Kent
Hydrogen Bonds At The Protein-Inhibitor Interface In The Hiv-1 Protease / Inhibitors Complexes Probed By Total Chemical Synthesis And X-Ray Crystallography
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - [D25N]HIV-1 PROTEASE
    Chains: A, B
    EC Number: 3.4.23.16
    Engineered: YES
    Other Details: TOTAL CHEMICAL SYNTHESIS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric Unit (5, 13)
No.NameCountTypeFull Name
12NC1Ligand/IonN-{(2S)-2-[(N-ACETYL-L-THREONYL-L-ISOLEUCYL)AMINO]HEXYL}-L-NORLEUCYL-L-GLUTAMINYL-N~5~-[AMINO(IMINIO)METHYL]-L-ORNITHINAMIDE
2ABA4Mod. Amino AcidALPHA-AMINOBUTYRIC ACID
3NLE4Mod. Amino AcidNORLEUCINE
4SO42Ligand/IonSULFATE ION
5YCM2Mod. Amino AcidS-(2-AMINO-2-OXOETHYL)-L-CYSTEINE
Biological Unit 1 (5, 8)
No.NameCountTypeFull Name
12NC1Ligand/IonN-{(2S)-2-[(N-ACETYL-L-THREONYL-L-ISOLEUCYL)AMINO]HEXYL}-L-NORLEUCYL-L-GLUTAMINYL-N~5~-[AMINO(IMINIO)METHYL]-L-ORNITHINAMIDE
2ABA2Mod. Amino AcidALPHA-AMINOBUTYRIC ACID
3NLE2Mod. Amino AcidNORLEUCINE
4SO42Ligand/IonSULFATE ION
5YCM1Mod. Amino AcidS-(2-AMINO-2-OXOETHYL)-L-CYSTEINE
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
12NC-1Ligand/IonN-{(2S)-2-[(N-ACETYL-L-THREONYL-L-ISOLEUCYL)AMINO]HEXYL}-L-NORLEUCYL-L-GLUTAMINYL-N~5~-[AMINO(IMINIO)METHYL]-L-ORNITHINAMIDE
2ABA2Mod. Amino AcidALPHA-AMINOBUTYRIC ACID
3NLE2Mod. Amino AcidNORLEUCINE
4SO4-1Ligand/IonSULFATE ION
5YCM1Mod. Amino AcidS-(2-AMINO-2-OXOETHYL)-L-CYSTEINE
Biological Unit 3 (5, 13)
No.NameCountTypeFull Name
12NC1Ligand/IonN-{(2S)-2-[(N-ACETYL-L-THREONYL-L-ISOLEUCYL)AMINO]HEXYL}-L-NORLEUCYL-L-GLUTAMINYL-N~5~-[AMINO(IMINIO)METHYL]-L-ORNITHINAMIDE
2ABA4Mod. Amino AcidALPHA-AMINOBUTYRIC ACID
3NLE4Mod. Amino AcidNORLEUCINE
4SO42Ligand/IonSULFATE ION
5YCM2Mod. Amino AcidS-(2-AMINO-2-OXOETHYL)-L-CYSTEINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:25 , GLY A:27 , ALA A:28 , ASP A:29 , ASP A:30 , ILE A:47 , GLY A:48 , GLY A:49 , ILE A:50 , PHE A:53 , VAL A:82 , ILE A:84 , HOH A:101 , HOH A:107 , HOH A:109 , HOH A:112 , HOH A:118 , HOH A:128 , HOH A:139 , HOH A:148 , LEU B:23 , ASN B:25 , GLY B:27 , ALA B:28 , ASP B:29 , ASP B:30 , NLE B:46 , ILE B:47 , GLY B:48 , GLY B:49 , ILE B:50 , PHE B:53 , PRO B:81 , ILE B:84 , HOH B:121BINDING SITE FOR RESIDUE 2NC A 100
2AC2SOFTWARELEU A:10 , GLU A:21 , ALA A:22 , VAL A:82 , ASN A:83 , HOH A:106BINDING SITE FOR RESIDUE SO4 A 401
3AC3SOFTWARETHR A:12 , ILE A:13 , ARG A:14 , LEU A:19 , TRP A:42 , PRO A:44 , GLU A:65 , ILE A:66 , ABA A:67 , GLY A:68BINDING SITE FOR RESIDUE SO4 A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IA9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3IA9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IA9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IA9)

(-) Exons   (0, 0)

(no "Exon" information available for 3IA9)

(-) Sequences/Alignments

Asymmetric 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:99
 aligned with O38732_9HIV1 | O38732 from UniProtKB/TrEMBL  Length:99

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
          O38732_9HIV1    1 PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  3ia9 A  1 PQITLWKRPLVTIRIGGQLKEALLNTGADDTVIEElNLPGcWKPKlIGGIGGFIKVRQYDQIPVEIaGHKAIGTVLVGPTPVNIIGRNLLTQIGaTLNF 99
                                    10        20        30     |  40|    |  50        60      | 70        80        90    |    
                                                              36-NLE|    |                   67-ABA                      95-ABA
                                                                   41-YCM|                                                     
                                                                        46-NLE                                                 


Chain B from PDB  Type:PROTEIN  Length:99
 aligned with O38732_9HIV1 | O38732 from UniProtKB/TrEMBL  Length:99

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
          O38732_9HIV1    1 PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  3ia9 B  1 PQITLWKRPLVTIRIGGQLKEALLNTGADDTVIEElNLPGcWKPKlIGGIGGFIKVRQYDQIPVEIaGHKAIGTVLVGPTPVNIIGRNLLTQIGaTLNF 99
                                    10        20        30     |  40|    |  50        60      | 70        80        90    |    
                                                              36-NLE|    |                   67-ABA                      95-ABA
                                                                   41-YCM|                                                     
                                                                        46-NLE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3IA9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IA9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IA9)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O38732_9HIV1 | O38732)
molecular function
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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  3ia9
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  O38732_9HIV1 | O38732
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  3.4.23.16
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 Related Entries

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

UniProtKB/Swiss-Prot
        O38732_9HIV1 | O38732: 2i0a 2i0d 2nxd 2nxl 2nxm 2psu 2psv 2q3k 2q54 2q55 2q5k 2qhy 2qhz 2qi0 2qi1 2qi3 2qi4 2qi5 2qi6 2qi7 3gi4 3gi5 3gi6
UniProtKB/TrEMBL
        O38732_9HIV1 | O38732: 3dck 3dcr 3hzc 3i2l 3sa3 3sa4 3sa5 3sa6 3sa7 3sa8 3sa9 3saa 3sab 3sac

(-) Related Entries Specified in the PDB File

3fsm 3hau 3haw 3hbo 3hdk 3hlo