2WPO - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   HCMV PROTEASE INHIBITOR COMPLEX

Authors :   L. Tong, C. Qian, M. -J. Massariol, R. Deziel, C. Yoakim, L. Lagace

Date :   04 Aug 98 (Deposition) - 04 Aug 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Viral Protease, Hydrolase-Hydrolase Inhibitor Complex, Coat Protein, Serine Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Tong, C. Qian, M. J. Massariol, R. Deziel, C. Yoakim, L. Lagace
Conserved Mode Of Peptidomimetic Inhibition And Substrate Recognition Of Human Cytomegalovirus Protease.
Nat. Struct. Biol. V. 5 819 1998
PubMed-ID: 9731777 | Reference-DOI: 10.1038/1860
(for further references see the PDB file header)

Molecule 1 - HUMAN CYTOMEGALOVIRUS PROTEASE
	Chains	:	A, B, C, D
	EC Number	:	3.4.21.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Common	:	HUMAN CYTOMEGALOVIRUS
	Organism Scientific	:	HUMAN HERPESVIRUS 5
	Organism Taxid	:	10359

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	01E	4	Ligand/Ion	(2S)-2-(3,3-DIMETHYLBUTANOYLAMINO)-N-[(2S)-1-[[(2S,3S)-3-HYDROXY-4-[(4-IODOPHENYL)METHYLAMINO]-4-OXO-BUTAN-2-YL]AMINO]-1,4-DIOXO-4-PYRROL-1-YL-BUTAN-2-YL]-3,3-DIMETHYL-BUTANAMIDE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	01E	2	Ligand/Ion	(2S)-2-(3,3-DIMETHYLBUTANOYLAMINO)-N-[(2S)-1-[[(2S,3S)-3-HYDROXY-4-[(4-IODOPHENYL)METHYLAMINO]-4-OXO-BUTAN-2-YL]AMINO]-1,4-DIOXO-4-PYRROL-1-YL-BUTAN-2-YL]-3,3-DIMETHYL-BUTANAMIDE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	01E	2	Ligand/Ion	(2S)-2-(3,3-DIMETHYLBUTANOYLAMINO)-N-[(2S)-1-[[(2S,3S)-3-HYDROXY-4-[(4-IODOPHENYL)METHYLAMINO]-4-OXO-BUTAN-2-YL]AMINO]-1,4-DIOXO-4-PYRROL-1-YL-BUTAN-2-YL]-3,3-DIMETHYL-BUTANAMIDE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:31 , HIS A:63 , SER A:132 , LEU A:133 , SER A:134 , SER A:135 , ARG A:136 , ARG A:137 , LYS A:156 , CYS A:161 , VAL A:163 , GLY A:164 , ARG A:165 , ILE A:231	BINDING SITE FOR RESIDUE 01E A 257
2	AC2	SOFTWARE	GLU B:31 , HIS B:63 , SER B:132 , LEU B:133 , SER B:134 , SER B:135 , ARG B:136 , LYS B:156 , CYS B:161 , VAL B:163 , GLY B:164 , ARG B:165 , ILE B:231	BINDING SITE FOR RESIDUE 01E B 257
3	AC3	SOFTWARE	GLU C:31 , HIS C:63 , SER C:132 , LEU C:133 , SER C:134 , SER C:135 , ARG C:136 , LYS C:156 , CYS C:161 , GLY C:164 , ARG C:165 , ILE C:231	BINDING SITE FOR RESIDUE 01E C 257
4	AC4	SOFTWARE	GLU D:31 , HIS D:63 , SER D:132 , LEU D:133 , SER D:134 , SER D:135 , ARG D:136 , LYS D:156 , CYS D:161 , VAL D:163 , GLY D:164 , ARG D:165 , ILE D:231	BINDING SITE FOR RESIDUE 01E D 257

(no "SS Bond" information available for 2WPO)

(no "Cis Peptide Bond" information available for 2WPO)

(no "SAP(SNP)/Variant" information available for 2WPO)

(no "PROSITE Motif" information available for 2WPO)

(no "Exon" information available for 2WPO)

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:230
 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 d2wpoa_ A: Human cytomegalovirus protease                                                                                                                                                                                                                     SCOP domains
               CATH domains 2wpoA00 A:4-256 Serine Protease, Human Cyto      megalovirus Protease; Chain A                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...eeeeeeee........hhh...hhhhhhhhhh.------.....eeee......eeeeeeeeeee..eeeeeeee..hhhhhhhhhhhhh.hhhhh.........hhhhhhhhh..eeeeee........--------...eeeeeee..........eee..hhhhhhh.....hhhhhhhhhhh.---------........hhhhhhhhhhhhh...hhhhhhhhhhhh.hhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wpo A   4 DEQQSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWLHAQ------LSVALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRRCDDVEQ--------TTPFKHVALCSVGRRRGTLAVYGRDPEWVMQRFPDLTAADRDGLRAQWQ---------SGDPFRSDSYGLLGNSVDAMYIRERLPKLRYDKQLVGVTERESYVKA 256
                                    13        23        33        43  |     53        63        73        83        93       103       113       123       133       143       153       163       173       183       193      |  -      |213       223       233       243       253   
                                                                     46     53                                                                                       143      152                                             200       210

Chain B from PDB  Type:PROTEIN  Length:230
 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 d2wpob_ B: Human cytomegalovirus protease                                                                                                                                                                                                                     SCOP domains
               CATH domains 2wpoB00 B:4-256 Serine Protease, Human Cyto      megalovirus Protease; Chain A                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...eeeeeeee........hhh...hhhhhhhhhh.------.....eeee......eeeeeeeeeee..eeeeeeee..hhhhhhhhhhhhh.hhhhh.........hhhhhhhhh..eeeeee........--------...eeeeeee..........eee..hhhhhhh.....hhhhhhhhhhh.---------........hhhhhhhhhhhhh...hhhhhhhhhhhh.hhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wpo B   4 DEQQSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWLHAQ------LSVALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRRCDDVEQ--------TTPFKHVALCSVGRRRGTLAVYGRDPEWVMQRFPDLTAADRDGLRAQWQ---------SGDPFRSDSYGLLGNSVDAMYIRERLPKLRYDKQLVGVTERESYVKA 256
                                    13        23        33        43  |     53        63        73        83        93       103       113       123       133       143       153       163       173       183       193      |  -      |213       223       233       243       253   
                                                                     46     53                                                                                       143      152                                             200       210

Chain C from PDB  Type:PROTEIN  Length:230
 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 d2wpoc_ C: Human cytomegalovirus protease                                                                                                                                                                                                                     SCOP domains
               CATH domains 2wpoC00 C:4-256 Serine Protease, Human Cyto      megalovirus Protease; Chain A                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...eeeeeeee........hhh...hhhhhhhhhh.------.....eeee......eeeeeeeeeee..eeeeeeee..hhhhhhhhhhhhh.hhhhh.........hhhhhhhhh..eeeeee........--------...eeeeeee..........eee..hhhhhhh.....hhhhhhhhhhh.---------........hhhhhhhhhhhhh...hhhhhhhhhhhh.hhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wpo C   4 DEQQSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWLHAQ------LSVALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRRCDDVEQ--------TTPFKHVALCSVGRRRGTLAVYGRDPEWVMQRFPDLTAADRDGLRAQWQ---------SGDPFRSDSYGLLGNSVDAMYIRERLPKLRYDKQLVGVTERESYVKA 256
                                    13        23        33        43  |     53        63        73        83        93       103       113       123       133       143       153       163       173       183       193      |  -      |213       223       233       243       253   
                                                                     46     53                                                                                       143      152                                             200       210

Chain D from PDB  Type:PROTEIN  Length:230
 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 d2wpod_ D: Human cytomegalovirus protease                                                                                                                                                                                                                     SCOP domains
               CATH domains 2wpoD00 D:4-256 Serine Protease, Human Cyto      megalovirus Protease; Chain A                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...eeeeeeee........hhh...hhhhhhhhhh.------.....eeee......eeeeeeeeeee..eeeeeeee..hhhhhhhhhhhhh.hhhhh.........hhhhhhhhh..eeeeee........--------...eeeeeee..........eee..hhhhhhh.....hhhhhhhhhhh.---------........hhhhhhhhhhhhh...hhhhhhhhhhhh.hhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wpo D   4 DEQQSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWLHAQ------LSVALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRRCDDVEQ--------TTPFKHVALCSVGRRRGTLAVYGRDPEWVMQRFPDLTAADRDGLRAQWQ---------SGDPFRSDSYGLLGNSVDAMYIRERLPKLRYDKQLVGVTERESYVKA 256
                                    13        23        33        43  |     53        63        73        83        93       103       113       123       133       143       153       163       173       183       193      |  -      |213       223       233       243       253   
                                                                     46     53                                                                                       143      152                                             200       210

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Herpes virus serine proteinase, assemblin (20)

Superfamily: Herpes virus serine proteinase, assemblin (20)

Family: Herpes virus serine proteinase, assemblin (20)

Protein domain: Human cytomegalovirus protease (15)

Human cytomegalovirus [TaxId: 10359] (15)

1a	d2wpoa_	A:
1b	d2wpob_	B:
1c	d2wpoc_	C:
1d	d2wpod_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: Serine Protease, Human Cytomegalovirus Protease; Chain A (20)

Homologous Superfamily: Serine Protease, Human Cytomegalovirus Protease; Chain A (20)

Human cytomegalovirus. (1)

1a	2wpoA00	A:4-256
1b	2wpoB00	B:4-256
1c	2wpoC00	C:4-256
1d	2wpoD00	D:4-256

(no "Pfam Domain" information available for 2WPO)

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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2wpo)

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	2wpo
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	3.4.21.-
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	SCAF_HCMVA \| P16753	:	1cmv 1id4 1iec 1ied 1ief 1ieg 1jq6 1jq7 1lay 1njt 1nju 1nkk 1nkm 1wpo

(no "Related Entries Specified in the PDB File" available for 2WPO)

Description

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Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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