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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 :  02 Jan 03  (Deposition) - 11 Feb 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
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  (5, 20)

Asymmetric Unit (5, 20)
No.NameCountTypeFull Name
1ACE4Mod. Amino AcidACETYL GROUP
2CFT4Mod. Amino AcidTRIFLUOROMETHANE
3CL4Ligand/IonCHLORIDE ION
4DMH4Mod. Amino AcidN4,N4-DIMETHYL-ASPARAGINE
5DMK4Mod. Amino Acid3,3-DIMETHYL ASPARTIC ACID
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2CFT2Mod. Amino AcidTRIFLUOROMETHANE
3CL-1Ligand/IonCHLORIDE ION
4DMH2Mod. Amino AcidN4,N4-DIMETHYL-ASPARAGINE
5DMK2Mod. Amino Acid3,3-DIMETHYL ASPARTIC ACID
Biological Unit 2 (4, 8)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2CFT2Mod. Amino AcidTRIFLUOROMETHANE
3CL-1Ligand/IonCHLORIDE ION
4DMH2Mod. Amino AcidN4,N4-DIMETHYL-ASPARAGINE
5DMK2Mod. Amino Acid3,3-DIMETHYL ASPARTIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:62 , CYS A:161 , SER A:162 , ASN A:224BINDING SITE FOR RESIDUE CL A 257
2AC2SOFTWAREASN B:362 , CYS B:461 , SER B:462 , ASN B:524BINDING SITE FOR RESIDUE CL B 2
3AC3SOFTWAREASN C:1062 , CYS C:1161 , SER C:1162 , ASN C:1224BINDING SITE FOR RESIDUE CL C 1
4AC4SOFTWAREASN D:1362 , CYS D:1461 , SER D:1462 , ASN D:1524BINDING SITE FOR RESIDUE CL D 4
5AC5SOFTWAREGLU A:31 , HIS A:63 , SER A:132 , LEU A:133 , SER A:134 , SER A:135 , ARG A:136 , ARG A:137 , GLY A:164 , ARG A:165 , ARG A:166 , HOH A:273 , HOH A:276 , HOH E:245BINDING SITE FOR CHAIN E OF PEPTIDOMIMETIC INHIBITOR
6AC6SOFTWAREHOH B:38 , HOH B:74 , GLU B:331 , HIS B:363 , SER B:432 , LEU B:433 , SER B:434 , SER B:435 , ARG B:436 , ARG B:437 , GLY B:464 , ARG B:465 , HOH F:98BINDING SITE FOR CHAIN F OF PEPTIDOMIMETIC INHIBITOR
7AC7SOFTWAREHOH C:244 , GLU C:1031 , HIS C:1063 , SER C:1132 , LEU C:1133 , SER C:1134 , SER C:1135 , ARG C:1136 , ARG C:1137 , GLY C:1164 , ARG C:1165 , HOH G:97BINDING SITE FOR CHAIN G OF PEPTIDOMIMETIC INHIBITOR
8AC8SOFTWAREHOH D:70 , GLU D:1331 , HIS D:1363 , SER D:1432 , LEU D:1433 , SER D:1434 , SER D:1435 , ARG D:1436 , ARG D:1437 , GLY D:1464 , ARG D:1465 , HOH H:140BINDING SITE FOR CHAIN H OF PEPTIDOMIMETIC INHIBITOR

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NJT)

(-) 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:226
 aligned with SCAF_HCMVA | P16753 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:254
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252    
          SCAF_HCMVA      3 MDEQQSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWLHAQGQGQPSLSVALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRRCDDVEAATSLSGSETTPFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQRCGSTAVDASGDPFRSDSYGLLGNSVDALYIRERLPKLRYDKQLVGVTERESYVKA  256
               SCOP domains d1njta_ A: Human cytomegalovirus protease                                                                                                                                                                                                                      SCOP domains
               CATH domains 1njtA00 A:3-256 Serine Protease, Human Cytom        egalovirus Protease; Chain A                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh..eeeeeeeee......hhhhh.hhhhhhhhhhh.--------...eeee......eeeeeeeeeee..eeeeeeee.hhhhhhhhhhhhh.hhhhhhh.......hhhhhhhhhhh.eeeeee....-------------..eeeeeee..........eee.hhhhhhh.....hhhhhhhhhhhhhhhh-------......hhhhhhhhhhhhh...hhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1njt A    3 MDEQQSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWLHAQ--------VALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRRCD-------------TPFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQRCG-------GDPFRSDSYGLLGNSVDALYIRERLPKLRYDKQLVGVTERESYVKA  256
                                    12        22        32        42   |     -  |     62        72        82        92       102       112       122       132      |  -         -|      162       172       182       192       202|      212       222       232       242       252    
                                                                      46       55                                                                                 139           153                                               203     211                                             


Chain B from PDB  Type:PROTEIN  Length:227
 aligned with SCAF_HCMVA | P16753 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:255
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     
          SCAF_HCMVA      2 TMDEQQSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWLHAQGQGQPSLSVALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRRCDDVEAATSLSGSETTPFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQRCGSTAVDASGDPFRSDSYGLLGNSVDALYIRERLPKLRYDKQLVGVTERESYVKA  256
               SCOP domains d1njtb_ B: Human cytomegalovirus protease                                                                                                                                                                                                                       SCOP domains
               CATH domains 1njtB00 B:302-556 Serine Protease, Human Cyto         megalovirus Protease; Chain A                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh..eeeeeeeee......hhhhh.hhhhhhhhhhhh---------..eeee......eeeeeeeeeee..eeeeeeee.hhhhhhhhhhhhh.hhhhhhh.......hhhhhhhhhhh.eeeeee....------------...eeeeeee..........eee.hhhhhhh.....hhhhhhhhhhhhhhh-------.......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1njt B  302 TMDEQQSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWLHAQ---------ALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRRCD------------TTPFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQRC-------SGDPFRSDSYGLLGNSVDALYIRERLPKLRYDKQLVGVTERESYVKA  556
                                   311       321       331       341    |    -    |  361       371       381       391       401       411       421       431       | -         -|      461       471       481       491       501|      511       521       531       541       551     
                                                                      346       356                                                                                439          452                                               502     510                                              


Chain C 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 d1njtc_ C: Human cytomegalovirus protease                                                                                                                                                                                                                     SCOP domains
               CATH domains 1njtC00 C:1004-1256 Serine Protease, Human           Cytomegalovirus Protease; Chain A                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh..eeeeeeeee......hhhhh.hhhhhhhhhhh----------..eeee......eeeeeeeeeee..eeeeeeee.hhhhhhhhhhhhh.hhhhhhh.......hhhhhhhhhhh.eeeeee....------------...eeeeeee..........eee.hhhhhhh.....hhhhhhhhhhhhh---------.......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1njt C 1004 DEQQSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWLHA----------ALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRRCD------------TTPFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQ---------SGDPFRSDSYGLLGNSVDALYIRERLPKLRYDKQLVGVTERESYVKA 1256
                                  1013      1023      1033      1043 |       -  |   1063      1073      1083      1093      1103      1113      1123      1133     |   -      1153      1163      1173      1183      1193      |  -      1213      1223      1233      1243      1253   
                                                                  1045       1056                                                                               1139         1152                                            1200      1210                                              


Chain D from PDB  Type:PROTEIN  Length:223
 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 d1njtd_ D: Human cytomegalovirus protease                                                                                                                                                                                                                     SCOP domains
               CATH domains 1njtD00 D:1304-1556 Serine Protease, Human          Cytomegalovirus Protease; Chain A                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh..eeeeeeeee......hhhhh.hhhhhhhhhhh---------...eeee......eeeeeeeeeee..eeeeeeee.hhhhhhhhhhhhh.hhhhhhh.......hhhhhhhhhhh.eeeeee...-------------...eeeeeee..........eee.hhhhhhh.....hhhhhhhhhhhhh--------........hhhhhhhhhhhhh...hhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1njt D 1304 DEQQSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWLHA---------VALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRRC-------------TTPFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQ--------ASGDPFRSDSYGLLGNSVDALYIRERLPKLRYDKQLVGVTERESYVKA 1556
                                  1313      1323      1333      1343 |       - |    1363      1373      1383      1393      1403      1413      1423      1433    |    -      1453      1463      1473      1483      1493      |  -     |1513      1523      1533      1543      1553   
                                                                  1345      1355                                                                               1438          1452                                            1500     1509                                               


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
                1njt 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
                1njt 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
                1njt 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
                1njt 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 1NJT)

(-) 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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  1njt
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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 1nju 1nkk 1nkm 1wpo 2wpo

(-) Related Entries Specified in the PDB File

1nju 1nkk 1nkm 2wpo