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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 :  2.60
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,E,F  (1x)
Biol. Unit 2:  C,D,G,H  (1x)
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 - CAPSID PROTEIN P40
    Chains: A, B, C, D
    EC Number: 3.4.21.97
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: ASSEMBLIN
    Gene: UL80 OR APNG
    Mutation: YES
    Organism Common: HUMAN CYTOMEGALOVIRUS
    Organism Scientific: HUMAN HERPESVIRUS 5
    Organism Taxid: 10359
    Synonym: PROTEASE, CAPSID ASSEMBLY PROTEIN
 
Molecule 2 - PEPTIDOMIMETIC INHIBITOR
    Chains: E, F, G, H
    Engineered: YES
    Other Details: RESIDUE PEPTIDE OF THE PEPTIDOMIMETIC INHIBITOR WAS CHEMICALLY SYNTHESIZED.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB  EF  
Biological Unit 2 (1x):   CD  GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric Unit (4, 16)
No.NameCountTypeFull Name
1ACE4Mod. Amino AcidACETYL GROUP
2CFT4Mod. Amino AcidTRIFLUOROMETHANE
3DMH4Mod. Amino AcidN4,N4-DIMETHYL-ASPARAGINE
4DMK4Mod. Amino Acid3,3-DIMETHYL ASPARTIC ACID
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2CFT2Mod. Amino AcidTRIFLUOROMETHANE
3DMH2Mod. Amino AcidN4,N4-DIMETHYL-ASPARAGINE
4DMK2Mod. Amino Acid3,3-DIMETHYL ASPARTIC ACID
Biological Unit 2 (4, 8)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2CFT2Mod. Amino AcidTRIFLUOROMETHANE
3DMH2Mod. Amino AcidN4,N4-DIMETHYL-ASPARAGINE
4DMK2Mod. Amino Acid3,3-DIMETHYL ASPARTIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:31 , HIS A:63 , SER A:132 , LEU A:133 , SER A:134 , SER A:135 , ARG A:136 , ARG A:137 , CYS A:161 , GLY A:164 , ARG A:165 , HOH A:2051 , HOH A:2246 , HOH E:2138BINDING SITE FOR CHAIN E OF PEPTIDOMIMETIC INHIBITOR
2AC2SOFTWAREARG B:331 , HIS B:363 , SER B:432 , LEU B:433 , SER B:434 , SER B:435 , ARG B:436 , ARG B:437 , VAL B:463 , GLY B:464 , ARG B:465 , ARG B:466 , HOH B:2092 , HOH F:2022 , HOH F:2109BINDING SITE FOR CHAIN F OF PEPTIDOMIMETIC INHIBITOR
3AC3SOFTWAREARG C:1031 , HIS C:1063 , SER C:1132 , LEU C:1133 , SER C:1134 , SER C:1135 , ARG C:1136 , ARG C:1137 , CYS C:1161 , GLY C:1164 , ARG C:1165 , HOH C:2098 , HOH C:2127 , HOH G:2073BINDING SITE FOR CHAIN G OF PEPTIDOMIMETIC INHIBITOR
4AC4SOFTWAREARG D:1331 , HIS D:1363 , LEU D:1431 , SER D:1432 , LEU D:1433 , SER D:1434 , SER D:1435 , ARG D:1436 , ARG D:1437 , GLY D:1464 , ARG D:1465 , ARG D:1466 , HOH D:2052 , HOH D:2057 , HOH D:2234 , HOH H:2151BINDING SITE FOR CHAIN H OF PEPTIDOMIMETIC INHIBITOR

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NKK)

(-) 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:222
 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 d1nkka_ A: Human cytomegalovirus protease                                                                                                                                                                                                                     SCOP domains
               CATH domains 1nkkA00 A:4-256 Serine Protease, Human Cyto        megalovirus Protease; Chain A                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee......hhhhh.hhhhhhhhhhhh--------...eeee..eeeeeeeeeeeeeee..eeeeeeee.hhhhhhhhhhhhh.hhhhhh........hhhhhhhhhhh.eeeeee..--------------...eeeeeee..........eee.hhhhhhh.....hhhhhhhhhhhhhh---------......hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1nkk A    4 DEQQSQAVAPVYVGGFLARYDQSPDEARLLLPRDVVEHWLHAQ--------VALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRR--------------TTPFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQR---------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       55                                                                               137            152                                              201       211                                             


Chain B from PDB  Type:PROTEIN  Length:226
 aligned with SCAF_HCMVA | P16753 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:252
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254  
          SCAF_HCMVA      5 EQQSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWLHAQGQGQPSLSVALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRRCDDVEAATSLSGSETTPFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQRCGSTAVDASGDPFRSDSYGLLGNSVDALYIRERLPKLRYDKQLVGVTERESYVKA  256
               SCOP domains d1nkkb_ B: Human cytomegalovirus protease                                                                                                                                                                                                                    SCOP domains
               CATH domains 1nkkB00 B:305-556 Serine Protease, Human C        ytomegalovirus Protease; Chain A                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeeeeee......hhhhh.hhhhhhhhhhhh--------...eeee......eeeeeeeeeee..eeeeeeee.hhhhhhhhhhhhh.hhhhhh........hhhhhhhhhhh.eeeeee....-----------....eeeeeee..........eee.hhhhhhh.....hhhhhhhhhhhhhhhh-------......hhhhhhhhhhhhhh..hhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1nkk B  305 EQQSQAVAPVYVGGFLARYDQSPDEARLLLPRDVVEHWLHAQ--------VALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRRCD-----------ETTPFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQRCG-------GDPFRSDSYGLLGNSVDALYIRERLPKLRYDKQLVGVTERESYVKA  556
                                   314       324       334       344 |       -|      364       374       384       394       404       414       424       434    |    -      |454       464       474       484       494        |-      |514       524       534       544       554  
                                                                   346      355                                                                                 439         451                                                 503     511                                             


Chain C from PDB  Type:PROTEIN  Length:226
 aligned with SCAF_HCMVA | P16753 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:251
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255 
          SCAF_HCMVA      6 QQSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWLHAQGQGQPSLSVALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRRCDDVEAATSLSGSETTPFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQRCGSTAVDASGDPFRSDSYGLLGNSVDALYIRERLPKLRYDKQLVGVTERESYVKA  256
               SCOP domains d1nkkc_ C: Human cytomegalovirus protease                                                                                                                                                                                                                   SCOP domains
               CATH domains 1nkkC00 C:1006-1256 Serine Protease, Huma        n Cytomegalovirus Protease; Chain A                                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..eeeeeeeee......hhhhh.hhhhhhhhhhhh--------...eeee......eeeeeeeeeee..eeeeeeee.hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.eeeeee......---------....eeeeeee..........eee.hhhhhhh.....hhhhhhhhhhhhh..--------......hhhhhhhhhhhhh...hhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1nkk C 1006 QQSQAVAPVYVGGFLARYDQSPDEARLLLPRDVVEHWLHAQ--------VALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRRCDDV---------ETTPFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQRC--------GDPFRSDSYGLLGNSVDALYIRERLPKLRYDKQLVGVTERESYVKA 1256
                                  1015      1025      1035      1045|     1055      1065      1075      1085      1095      1105      1115      1125      1135     |   -     |1155      1165      1175      1185      1195      |  -     |1215      1225      1235      1245      1255 
                                                                 1046     1055                                                                                  1141      1151                                               1202     1211                                             


Chain D 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 d1nkkd_ D: Human cytomegalovirus protease                                                                                                                                                                                                                     SCOP domains
               CATH domains 1nkkD00 D:1304-1556 Serine Protease, Human         Cytomegalovirus Protease; Chain A                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee......hhhhh.hhhhhhhhhhh.--------...eeee..eeeeeeeeeeeeeee..eeeeeeee.hhhhhhhhhhhhh.hhhhhh........hhhhhhhhhhh.eeeeee..---------------..eeeeeee..........eee.hhhhhhh.....hhhhhhhhhhhhh----------......hhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1nkk D 1304 DEQQSQAVAPVYVGGFLARYDQSPDEARLLLPRDVVEHWLHAQ--------VALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRR---------------TPFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQ----------GDPFRSDSYGLLGNSVDALYIRERLPKLRYDKQLVGVTERESYVKA 1556
                                  1313      1323      1333      1343  |      - |    1363      1373      1383      1393      1403      1413      1423      1433   |     -      1453      1463      1473      1483      1493      |  -      1513      1523      1533      1543      1553   
                                                                   1346     1355                                                                              1437            1453                                           1500       1511                                             


Chain E from PDB  Type:PROTEIN  Length:6
                                       
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ..ee.. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                1nkk E  260 xVdnAx  265
                            | || |
                          260-ACE|
                            262-DMK
                             263-DMH
                               265-CFT


Chain F from PDB  Type:PROTEIN  Length:6
                                       
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ..ee.. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                1nkk F  560 xVdnAx  565
                            | || |
                            | || |
                          560-ACE|
                            562-DMK
                             563-DMH
                               565-CFT


Chain G from PDB  Type:PROTEIN  Length:6
                                       
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ..ee.. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                1nkk G 1260 xVdnAx 1265
                            | || |
                            | || |
                         1260-ACE|
                           1262-DMK
                            1263-DMH
                              1265-CFT


Chain H from PDB  Type:PROTEIN  Length:6
                                       
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ..ee.. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                1nkk H 1560 xVdnAx 1565
                            | || |
                            | || |
                         1560-ACE|
                           1562-DMK
                            1563-DMH
                              1565-CFT
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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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  1nkk
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  SCAF_HCMVA | P16753
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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 1nkm 1wpo 2wpo

(-) Related Entries Specified in the PDB File

1njt 1nju 1nkm 2wpo