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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF KSHV PROTEASE IN COMPLEX WITH HEXAPEPTIDE PHOSPHONATE INHIBITOR

Authors :   A. Lazic, D. H. Goetz

Date :   28 Mar 07 (Deposition) - 25 Dec 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.73

Chains :   Asym./Biol. Unit : A,B,C,D

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

Reference :   A. Lazic, D. H. Goetz, A. M. Nomura, A. B. Marnett, C. S. Craik
Substrate Modulation Of Enzyme Activity In The Herpesvirus Protease Family.
J. Mol. Biol. V. 373 913 2007
PubMed-ID: 17870089 | Reference-DOI: 10.1016/J.JMB.2007.07.073

Molecule 1 - KSHV PROTEASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL21(DE3)GOLD
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AF010430
	Mutation	:	YES
	Organism Scientific	:	HUMAN HERPESVIRUS
	Organism Taxid	:	37296
	Strain	:	8

Molecule 2 - HEXAPEPTIDE PHOSPHONATE INHIBITOR
	Chains	:	C, D
	Engineered	:	YES
	Other Details	:	SOLID PHASE FMOC
	Synthetic	:	YES

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 9)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP
2	ACT	3	Ligand/Ion	ACETATE ION
3	GG7	2	Mod. Amino Acid	[(1R)-1-AMINOETHYL]PHOSPHONIC ACID
4	TBG	2	Mod. Amino Acid	3-METHYL-L-VALINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:12 , VAL A:14 , LEU A:25 , PRO A:27 , GLN A:60 , GLY A:64 , ILE A:65 , HOH A:643	BINDING SITE FOR RESIDUE ACT A 601
2	AC2	SOFTWARE	GLU A:100 , PRO A:101 , LEU A:102 , LEU A:103 , HIS A:152	BINDING SITE FOR RESIDUE ACT A 602
3	AC3	SOFTWARE	PRO B:39 , SER B:185 , HOH B:813 , HOH B:819	BINDING SITE FOR RESIDUE ACT B 603
4	AC4	SOFTWARE	GLU B:22 , HIS B:46 , SER B:114 , LEU B:115 , SER B:116 , SER B:117 , ILE B:118 , HIS B:119 , ARG B:121 , GLU B:122 , SER B:128 , GLY B:129 , PRO B:130 , GLN B:133 , GLY B:141 , ARG B:142 , ARG B:143 , HOH B:654 , HOH C:8 , HOH C:9 , HOH C:10 , HOH C:11 , HOH C:12 , HOH C:13 , HOH C:14 , HOH C:15 , HOH C:17	BINDING SITE FOR CHAIN C OF HEXAPEPTIDE PHOSPHONATE INHIBITOR
5	AC5	SOFTWARE	GLU A:22 , HIS A:46 , SER A:114 , LEU A:115 , SER A:116 , SER A:117 , ILE A:118 , HIS A:119 , GLU A:122 , PRO A:130 , GLY A:141 , ARG A:142 , ARG A:143 , HOH A:606 , HOH A:754 , HOH D:8 , HOH D:9 , HOH D:10 , HOH D:11 , HOH D:12 , HOH D:13	BINDING SITE FOR CHAIN D OF HEXAPEPTIDE PHOSPHONATE INHIBITOR

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

Asymmetric/Biological Unit

No.	Residues
1	Leu A:34	-	Pro A:35
2	Ser A:224	-	Pro A:225
3	Leu B:34	-	Pro B:35
4	Ser B:224	-	Pro B:225

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

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

(no "Exon" information available for 2PBK)

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:228
 aligned with O36607_HHV8 | O36607 from UniProtKB/TrEMBL  Length:535

    Alignment length:228
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222        
          O36607_HHV8     3 QGLYVGGFVDVVSCPKLEQELYLDPDQVTDYLPVTEPLPITIEHLPETEVGWTLGLFQVSHGIFCTGAITSPAFLELASRLADTSHVARAPVKNLPKEPLLEILHTWLPGLSLSSIHPRELSQTPSGPVFQHVSLCALGRRRGTVAVYGHDAEWVVSRFSSVSKSERAHILQHVSSCRLEDLSTPNFVSPLETLMAKAIDASFIRDRLDLLKTDRGVASILSPVYLKA 230
               SCOP domains d2pbka_ A: KSHV protease                                                                                                                                                                                                             SCOP domains
               CATH domains 2pbkA00 A:3-230 Serine Protease, Human Cytomegalovirus Protease; Chain A                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee......hhhhh.hhhhhhhhh......eeee........eeeeeeeee..eeeeeeee.hhhhhhhhhhhhhhh............hhhhhhhhhhh.eeeeeeehhhhhh.......eeeeeee..........eee.hhhhhhhh....hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pbk A   3 QGLYVGGFVDVVSCPKLEQELYLDPDQVTDYLPVTEPLPITIEHLPETEVGWTLGLFQVSHGIFCTGAITSPAFLELASRLADTSHVARAPVKNLPKEPLLEILHTWLPGLSLSSIHPRELSQTPSGPVFQHVSLCALGRRRGTVAVYGHDAEWVVSRFSSVSKSERAHILQHVSSCRLEDLSTPNFVSPLETLMAKAIDAGFIRDRLDLLKTDRGVASILSPVYLKA 230
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222

Chain B from PDB  Type:PROTEIN  Length:227
 aligned with O36607_HHV8 | O36607 from UniProtKB/TrEMBL  Length:535

    Alignment length:228
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222        
          O36607_HHV8     3 QGLYVGGFVDVVSCPKLEQELYLDPDQVTDYLPVTEPLPITIEHLPETEVGWTLGLFQVSHGIFCTGAITSPAFLELASRLADTSHVARAPVKNLPKEPLLEILHTWLPGLSLSSIHPRELSQTPSGPVFQHVSLCALGRRRGTVAVYGHDAEWVVSRFSSVSKSERAHILQHVSSCRLEDLSTPNFVSPLETLMAKAIDASFIRDRLDLLKTDRGVASILSPVYLKA 230
               SCOP domains d2pbkb_ B: KSHV protease                                                                                                                                                                                                             SCOP domains
               CATH domains 2pbkB00 B:3-230 Serine Protease, Human Cytomegalovirus Protease; Chain A                                                                                                                                                             CATH domains
           Pfam domains (1) -------------------Peptidase_S21-2pbkB01 B:22-230                                                                                                                                                                                    Pfam domains (1)
           Pfam domains (2) -------------------Peptidase_S21-2pbkB02 B:22-230                                                                                                                                                                                    Pfam domains (2)
         Sec.struct. author ...eeeeeeee......hhhhh.hhhhhhhhh......eeee........eeeeeeeee..eeeeeeee.hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.eeeeeee.hhhh..-.....eeeeeee..........eee.hhhhhhhh....hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pbk B   3 QGLYVGGFVDVVSCPKLEQELYLDPDQVTDYLPVTEPLPITIEHLPETEVGWTLGLFQVSHGIFCTGAITSPAFLELASRLADTSHVARAPVKNLPKEPLLEILHTWLPGLSLSSIHPRELSQ-PSGPVFQHVSLCALGRRRGTVAVYGHDAEWVVSRFSSVSKSERAHILQHVSSCRLEDLSTPNFVSPLETLMAKAIDAGFIRDRLDLLKTDRGVASILSPVYLKA 230
                                    12        22        32        42        52        62        72        82        92       102       112       122  | |  132       142       152       162       172       182       192       202       212       222        
                                                                                                                                                    125 |                                                                                                       
                                                                                                                                                      127

Chain C from PDB  Type:PROTEIN  Length:7
                                       
               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
                 2pbk C   1 xPVYvQx   7
                            |   | |
                            1-ACE |
                                5-TBG
                                  7-GG7

Chain D from PDB  Type:PROTEIN  Length:7
                                       
               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
                 2pbk D   1 xPVYvQx   7
                            |   | |
                            |   | |
                            1-ACE |
                                5-TBG
                                  7-GG7

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/Biological 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: KSHV protease (2)

Kaposi's sarcoma-associated herpesvirus [TaxId: 37296] (2)

1a	d2pbka_	A:
1b	d2pbkb_	B:

Asymmetric/Biological 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 herpesvirus 8. Organism_taxid: 37296. Strain: 8. (1)

1a	2pbkB00	B:3-230
1b	2pbkA00	A:3-230

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_SH (1)

Family: Peptidase_S21 (1)

Human herpesvirus 8 (HHV-8) (Kaposis sarcoma-associated herpesvirus) (1)

1a	Peptidase_S21-2pbkB01	B:22-230
1b	Peptidase_S21-2pbkB02	B:22-230

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (O36607_HHV8 | O36607)

molecular function
	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).
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Leu A:34 - Pro A:35	[ RasMol ]
		Leu B:34 - Pro B:35	[ RasMol ]
		Ser A:224 - Pro A:225	[ RasMol ]
		Ser B:224 - Pro B:225	[ RasMol ]

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	O36607_HHV8 \| O36607	:	4p2t
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	O36607_HHV8 \| O36607	:	1fl1 4p3h

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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