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(-) Description

Title :  CRYSTAL STRUCTURE OF HTLV PROTEASE COMPLEXED WITH STATINE-CONTAINING PEPTIDE INHIBITOR
 
Authors :  T. Satoh, M. Li, J. Nguyen, Y. Kiso, A. Wlodawer, A. Gustchina
Date :  25 Jan 10  (Deposition) - 14 Jul 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym. Unit :  A,B,C,D,E,F,I,J,K
Biol. Unit 1:  E,F,K  (1x)
Biol. Unit 2:  C,D,J  (1x)
Biol. Unit 3:  A,B,I  (1x)
Keywords :  Statine, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Satoh, M. Li, J. T. Nguyen, Y. Kiso, A. Gustchina, A. Wlodawer
Crystal Structures Of Inhibitor Complexes Of Human T-Cell Leukemia Virus (Htlv-1) Protease.
J. Mol. Biol. V. 401 626 2010
PubMed-ID: 20600105  |  Reference-DOI: 10.1016/J.JMB.2010.06.052

(-) Compounds

Molecule 1 - PROTEASE
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHTLVDELTA9
    Expression System Strain: ROSETTA2(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PRT
    Mutation: YES
    Organism Scientific: HUMAN T-LYMPHOTROPIC VIRUS 1
    Organism Taxid: 11908
 
Molecule 2 - STATINE-CONTAINING INHIBITOR
    Chains: I, J, K
    Engineered: YES

 Structural Features

(-) Chains, Units

  123456789
Asymmetric Unit : ABCDEFIJK
Biological Unit 1 (1x):     EF  K
Biological Unit 2 (1x):   CD   J 
Biological Unit 3 (1x): AB    I  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
2STA3Mod. Amino AcidSTATINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
2STA1Mod. Amino AcidSTATINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
2STA1Mod. Amino AcidSTATINE
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
2STA1Mod. Amino AcidSTATINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:14 , GLN A:16 , ARG A:77 , LEU A:78 , PRO A:79BINDING SITE FOR RESIDUE PEG A 117
2AC2SOFTWAREARG C:77 , LEU C:78 , PRO C:79BINDING SITE FOR RESIDUE PEG C 117
3AC3SOFTWAREGLN E:16 , ARG E:77 , PRO E:79BINDING SITE FOR RESIDUE PEG E 117
4AC4SOFTWAREARG A:10 , LEU A:30 , ASP A:32 , GLY A:34 , ALA A:35 , ASP A:36 , MET A:37 , THR A:54 , SER A:55 , VAL A:56 , LEU A:57 , TRP A:98 , ARG B:10 , ASP B:32 , GLY B:34 , ALA B:35 , ASP B:36 , SER B:55 , VAL B:56 , LEU B:57 , GLY B:58 , ALA B:59 , GLN B:62 , TRP B:98 , ILE B:100 , HOH I:18BINDING SITE FOR CHAIN I OF STATINE-CONTAINING INHIBITOR
5AC5SOFTWAREARG C:10 , ASP C:32 , GLY C:34 , ALA C:35 , ASP C:36 , MET C:37 , SER C:55 , VAL C:56 , LEU C:57 , GLY C:58 , ALA C:59 , LEU C:91 , TRP C:98 , ARG D:10 , ASP D:32 , GLY D:34 , ALA D:35 , ASP D:36 , MET D:37 , SER D:55 , VAL D:56 , LEU D:57 , GLY D:58 , ALA D:59 , GLN D:62 , LEU D:91 , TRP D:98 , HOH J:105 , HOH J:126 , HOH J:283 , HOH J:284BINDING SITE FOR CHAIN J OF STATINE-CONTAINING INHIBITOR
6AC6SOFTWAREARG E:10 , LEU E:30 , ASP E:32 , GLY E:34 , ALA E:35 , ASP E:36 , MET E:37 , SER E:55 , VAL E:56 , LEU E:57 , GLY E:58 , LEU E:91 , TRP E:98 , ARG F:10 , LEU F:30 , ASP F:32 , GLY F:34 , ALA F:35 , ASP F:36 , MET F:37 , SER F:55 , VAL F:56 , LEU F:57 , GLY F:58 , LEU F:91 , TRP F:98 , HOH K:100 , HOH K:192 , HOH K:285BINDING SITE FOR CHAIN K OF STATINE-CONTAINING INHIBITOR

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LIY)

(-) 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.....eee..eee..eee...eeee...eeee.......eee...eee......eehhhhhhhh..eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3liy 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......ee..eee..eee...eee....eeee.......eee...eee......eehhhhhhhh..eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3liy B   1 PVIPLDPARRPVIKAQVDTQTSHPKTIEALLDTGADMTVIPIALFSSNTPLKNTSVLGAGGQTQDHFKLTSLPVLIRLPFRTTPIVLTSCLVDTKNNWAIIGRDALQQCQGVLYLP 116
                                    10        20        30        40        50        60        70        80        90       100       110      


Chain C 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
                 3liy C   1 PVIPLDPARRPVIKAQVDTQTSHPKTIEALLDTGADMTVIPIALFSSNTPLKNTSVLGAGGQTQDHFKLTSLPVLIRLPFRTTPIVLTSCLVDTKNNWAIIGRDALQQCQGVLYLP 116
                                    10        20        30        40        50        60        70        80        90       100       110      


Chain D 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..eee..eee...eee....eeee.......eee...eee......eehhhhhhhh..eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3liy D   1 PVIPLDPARRPVIKAQVDTQTSHPKTIEALLDTGADMTVIPIALFSSNTPLKNTSVLGAGGQTQDHFKLTSLPVLIRLPFRTTPIVLTSCLVDTKNNWAIIGRDALQQCQGVLYLP 116
                                    10        20        30        40        50        60        70        80        90       100       110      


Chain E 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 .................................................................................................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3liy E   1 PVIPLDPARRPVIKAQVDTQTSHPKTIEALLDTGADMTVIPIALFSSNTPLKNTSVLGAGGQTQDHFKLTSLPVLIRLPFRTTPIVLTSCLVDTKNNWAIIGRDALQQCQGVLYLP 116
                                    10        20        30        40        50        60        70        80        90       100       110      


Chain F 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 (1) -----RVP-3liyF01 F:6-114                                                                                          -- Pfam domains (1)
           Pfam domains (2) -----RVP-3liyF02 F:6-114                                                                                          -- Pfam domains (2)
           Pfam domains (3) -----RVP-3liyF03 F:6-114                                                                                          -- Pfam domains (3)
           Pfam domains (4) -----RVP-3liyF04 F:6-114                                                                                          -- Pfam domains (4)
           Pfam domains (5) -----RVP-3liyF05 F:6-114                                                                                          -- Pfam domains (5)
           Pfam domains (6) -----RVP-3liyF06 F:6-114                                                                                          -- Pfam domains (6)
         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
                 3liy F   1 PVIPLDPARRPVIKAQVDTQTSHPKTIEALLDTGADMTVIPIALFSSNTPLKNTSVLGAGGQTQDHFKLTSLPVLIRLPFRTTPIVLTSCLVDTKNNWAIIGRDALQQCQGVLYLP 116
                                    10        20        30        40        50        60        70        80        90       100       110      


Chain I from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 3liy I 402 APQVxVMHP 410
                                |    
                              406-STA


Chain J from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 3liy J 402 APQVxVMH 409
                                |   
                              406-STA


Chain K from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 3liy K 402 APQVxVMH 409
                                |   
                              406-STA
   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 3LIY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Clan: Peptidase_AA (368)
(-)
Family: RVP (212)
(-)
Human T-lymphotropic virus 1 (6)
1aRVP-3liyF01F:6-114
1bRVP-3liyF02F:6-114
1cRVP-3liyF03F:6-114
1dRVP-3liyF04F:6-114
1eRVP-3liyF05F:6-114
1fRVP-3liyF06F:6-114

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (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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  3liy
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  Q82134_9DELA | Q82134
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 Related Entries

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

UniProtKB/TrEMBL
        Q82134_9DELA | Q82134: 3lin 3liq 3lit 3liv 3lix 3wsj 4ydf

(-) Related Entries Specified in the PDB File

2b7f 3lin 3liq 3lit 3liv 3lix