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(-) Description

Title :  COMPLEX STRUCTURE OF HCMV PROTEASE AND A PEPTIDOMIMETIC INHIBITOR
 
Authors :  R. Khayat, R. Batra, C. Qian, T. Halmos, M. Bailey, L. Tong
Date :  03 Jan 03  (Deposition) - 11 Feb 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protease, Peptidomimetic Inhibitor, Induced-Fit, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Khayat, R. Batra, C. Qian, T. Halmos, M. Bailey, L. Tong
Structural And Biochemical Studies Of Inhibitor Binding To Human Cytomegalovirus Protease
Biochemistry V. 42 885 2003
PubMed-ID: 12549906  |  Reference-DOI: 10.1021/BI027045S

(-) Compounds

Molecule 1 - ASSEMBLIN
    Chains: A, B
    EC Number: 3.4.21.97
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: UL80, APNG
    Mutation: YES
    Organism Common: HUMAN CYTOMEGALOVIRUS
    Organism Scientific: HUMAN HERPESVIRUS 5
    Organism Taxid: 10359
    Synonym: PROTEASE, CAPSID ASSEMBLY PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
10FP1Ligand/IonN-(6-AMINOHEXANOYL)-3-METHYL-L-VALYL-3-METHYL-L-VALYL-N~1~-[(2S,3S)-3-HYDROXY-4-OXO-4-{[(1R)-1-PHENYLPROPYL]AMINO}BUTAN-2-YL]-N~4~,N~4~-DIMETHYL-L-ASPARTAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:62 , HIS A:63 , SER A:132 , LEU A:133 , SER A:134 , SER A:135 , ARG A:136 , LYS A:156 , CYS A:161 , VAL A:163 , GLY A:164 , ARG A:165 , ILE A:231BINDING SITE FOR RESIDUE 0FP A 260

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NKM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NKM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NKM)

(-) Exons   (0, 0)

(no "Exon" information available for 1NKM)

(-) 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:220
 aligned with SCAF_HCMVA | P16753 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:253
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253   
           SCAF_HCMVA     4 DEQQSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWLHAQGQGQPSLSVALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRRCDDVEAATSLSGSETTPFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQRCGSTAVDASGDPFRSDSYGLLGNSVDALYIRERLPKLRYDKQLVGVTERESYVKA 256
               SCOP domains d1nkma_ A: Human cytomegalovirus protease                                                                                                                                                                                                                     SCOP domains
               CATH domains 1nkmA00 A:4-256 Serine Protease, Human Cyto         megalovirus Protease; Chain A                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..eeeeeeee.......hhhhh.hhhhhhhhhhh.---------..eeee..eeeeeeeeeeeeee....eeeeeee.hhhhhhhhhhhhh.hhhhhh........hhhhhhhhhhh.eeeee...--------------.....eeeee..........eee.hhhhhhh.....hhhhhhhhhhhhh----------......hhhhhhhhhhhhh...hhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nkm A   4 DEQQSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWLHAQ---------ALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRR--------------TTPFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQ----------GDPFRSDSYGLLGNSVDALYIRERLPKLRYDKQLVGVTERESYVKA 256
                                    13        23        33        43  |      -  |     63        73        83        93       103       113       123       133   |     -       153       163       173       183       193      |  -       213       223       233       243       253   
                                                                     46        56                                                                              137            152                                             200        211                                             


Chain B from PDB  Type:PROTEIN  Length:220
 aligned with SCAF_HCMVA | P16753 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:253
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253   
           SCAF_HCMVA     4 DEQQSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWLHAQGQGQPSLSVALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRRCDDVEAATSLSGSETTPFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQRCGSTAVDASGDPFRSDSYGLLGNSVDALYIRERLPKLRYDKQLVGVTERESYVKA 256
               SCOP domains d1nkmb_ B: Human cytomegalovirus protease                                                                                                                                                                                                                     SCOP domains
               CATH domains 1nkmB00 B:304-556 Serine Protease, Human Cy      tomegalovirus Protease; Chain A                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..eeeeeeeee......hhhhh.hhhhhhhhhh..------.....eeee......eeeeeeeeee...eeeeeeee.hhhhhhhhhhhhh.hhhhhh........hhhhhhhhhhh.eeeee------------------....eeeee..........eee.hhhhhhh.....hhhhhhhhhhhhh---------.......hhhhhhhhhhhhhh..hhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nkm B 304 DEQQSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWLHAQ------LSVALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLS------------------TPFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQ---------SGDPFRSDSYGLLGNSVDALYIRERLPKLRYDKQLVGVTERESYVKA 556
                                   313       323       333       343  |    353       363       373       383       393       403       413       423       433|        -       453       463       473       483       493      |  -      |513       523       533       543       553   
                                                                    346    353                                                                              434                453                                            500       510
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SCAF_HCMVA | P16753)
molecular function
    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.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.

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  1nkm
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  3.4.21.97
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 Related Entries

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

UniProtKB/Swiss-Prot
        SCAF_HCMVA | P16753: 1cmv 1id4 1iec 1ied 1ief 1ieg 1jq6 1jq7 1lay 1njt 1nju 1nkk 1wpo 2wpo

(-) Related Entries Specified in the PDB File

1njt 1nju 1nkk 2wpo