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(-) Description

Title :  HTLV-1 PROTEASE IN COMPLEX WITH THE HIV-1 PROTEASE INHIBITOR INDINAVIR
 
Authors :  M. Kuhnert, H. Steuber, W. E. Diederich
Date :  14 Mar 14  (Deposition) - 22 Oct 14  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (3x)
Keywords :  Retroviral Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kuhnert, H. Steuber, W. E. Diederich
Structural Basis For Htlv-1 Protease Inhibition By The Hiv- Protease Inhibitor Indinavir.
J. Med. Chem. V. 57 6266 2014
PubMed-ID: 25006983  |  Reference-DOI: 10.1021/JM500402C

(-) Compounds

Molecule 1 - PROTEASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-116
    Gene: PRT
    Mutation: YES
    Organism Scientific: HUMAN T-LYMPHOTROPIC VIRUS 1
    Organism Taxid: 11908

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric Unit (3, 15)
No.NameCountTypeFull Name
1MK11Ligand/IonN-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARYBUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE
2PG41Ligand/IonTETRAETHYLENE GLYCOL
3SO413Ligand/IonSULFATE ION
Biological Unit 1 (3, 15)
No.NameCountTypeFull Name
1MK11Ligand/IonN-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARYBUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE
2PG41Ligand/IonTETRAETHYLENE GLYCOL
3SO413Ligand/IonSULFATE ION
Biological Unit 2 (3, 45)
No.NameCountTypeFull Name
1MK13Ligand/IonN-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARYBUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE
2PG43Ligand/IonTETRAETHYLENE GLYCOL
3SO439Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:10 , ASP A:32 , GLY A:34 , ASP A:36 , MET A:37 , VAL A:39 , LEU A:91 , TRP A:98 , ILE A:100 , HOH A:308 , HOH A:329 , HOH A:336 , ARG B:10 , LEU B:30 , ASP B:32 , GLY B:34 , MET B:37 , VAL B:56 , TRP B:98BINDING SITE FOR RESIDUE MK1 A 201
02AC2SOFTWAREPRO A:4 , ARG A:9 , ARG A:10BINDING SITE FOR RESIDUE SO4 A 202
03AC3SOFTWAREPRO A:7 , ALA A:8 , ARG A:10 , ASP B:36BINDING SITE FOR RESIDUE SO4 A 203
04AC4SOFTWAREARG A:9 , HOH A:304BINDING SITE FOR RESIDUE SO4 A 204
05AC5SOFTWAREGLN A:16 , PRO A:24 , THR A:26 , SO4 A:206 , ASP B:18 , GLN B:20 , LEU B:75BINDING SITE FOR RESIDUE SO4 A 205
06AC6SOFTWAREGLN A:16 , THR A:26 , SO4 A:205 , PG4 A:212 , LEU B:75 , ARG B:77BINDING SITE FOR RESIDUE SO4 A 206
07AC7SOFTWAREGLN A:20 , GLN B:16 , PRO B:24 , LYS B:25 , THR B:26BINDING SITE FOR RESIDUE SO4 A 207
08AC8SOFTWARETHR A:83 , ILE A:85 , GLN A:108 , CYS A:109BINDING SITE FOR RESIDUE SO4 A 208
09AC9SOFTWAREVAL A:86 , GLN A:108 , LYS B:14BINDING SITE FOR RESIDUE SO4 A 209
10BC1SOFTWAREARG A:81 , THR A:82 , THR A:83BINDING SITE FOR RESIDUE SO4 A 210
11BC2SOFTWAREILE A:27 , GLU A:28 , ALA A:99 , SER B:71 , PRO B:73 , HOH B:304BINDING SITE FOR RESIDUE SO4 A 211
12BC3SOFTWAREGLN A:16 , ARG A:77 , LEU A:78 , PRO A:79 , ARG A:81 , SO4 A:206BINDING SITE FOR RESIDUE PG4 A 212
13BC4SOFTWARELYS B:14 , PRO B:79 , HOH B:318 , HOH B:329BINDING SITE FOR RESIDUE SO4 B 201
14BC5SOFTWAREARG B:81 , THR B:83 , GLN B:108 , CYS B:109BINDING SITE FOR RESIDUE SO4 B 202
15BC6SOFTWARESER A:71 , ILE B:27 , GLU B:28 , PRO B:41 , ALA B:99BINDING SITE FOR RESIDUE SO4 B 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WSJ)

(-) 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:116
 aligned with Q82134_9DELA | Q82134 from UniProtKB/TrEMBL  Length:125

    Alignment length:116
                                    10        20        30        40        50        60        70        80        90       100       110      
         Q82134_9DELA     1 PVIPLDPARRPVIKAQVDTQTSHPKTIEALLDTGADMTVLPIALFSSNTPLKNTSVLGAGGQTQDHFKLTSLPVLIRLPFRTTPIVLTSCLVDTKNNWAIIGRDALQQCQGVLYLP 116
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.......eeeeeee......eeeeeee.......eee.hhh......ee..ee....ee...eee....eeee.......eee...eee......eehhhhhhhh..eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3wsj A   1 PVIPLDPARRPVIKAQVDTQTSHPKTIEALLDTGADMTVIPIALFSSNTPLKNTSVLGAGGQTQDHFKLTSLPVLIRLPFRTTPIVLTSCLVDTKNNWAIIGRDALQQCQGVLYLP 116
                                    10        20        30        40        50        60        70        80        90       100       110      


Chain B from PDB  Type:PROTEIN  Length:116
 aligned with Q82134_9DELA | Q82134 from UniProtKB/TrEMBL  Length:125

    Alignment length:116
                                    10        20        30        40        50        60        70        80        90       100       110      
         Q82134_9DELA     1 PVIPLDPARRPVIKAQVDTQTSHPKTIEALLDTGADMTVLPIALFSSNTPLKNTSVLGAGGQTQDHFKLTSLPVLIRLPFRTTPIVLTSCLVDTKNNWAIIGRDALQQCQGVLYLP 116
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.......eeeeeee......eeeeeee.......eee.hhh.....eee..eee..eee...eeee...eeee.......eee...eee......eehhhhhhhh..eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3wsj B   1 PVIPLDPARRPVIKAQVDTQTSHPKTIEALLDTGADMTVIPIALFSSNTPLKNTSVLGAGGQTQDHFKLTSLPVLIRLPFRTTPIVLTSCLVDTKNNWAIIGRDALQQCQGVLYLP 116
                                    10        20        30        40        50        60        70        80        90       100       110
   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 3WSJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q82134_9DELA | Q82134)
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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 Related Entries

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        Q82134_9DELA | Q82134: 3lin 3liq 3lit 3liv 3lix 3liy 4ydf

(-) Related Entries Specified in the PDB File

3lix CRYSTAL STRUCTURE OF HTLV PROTEASE COMPLEXED WITH THE INHIBITOR KNI-10729