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(-) Description

Title :  CRYSTAL STRUCTURE OF KAPOSI'S SARCOMA-ASSOCIATED HERPESVIRUS (KSHV) PROTEASE IN COMPLEX WITH A DIMER DISRUPTOR
 
Authors :  J. E. Gable
Date :  04 Mar 14  (Deposition) - 16 Jul 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (2x),B (2x)
Keywords :  Protein-Protein Interaction Inhibition, Serine Protease, Inhibitor Complex, Beta Barrel And Alpha Helices (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. E. Gable, G. M. Lee, P. Jaishankar, B. R. Hearn, C. A. Waddling, A. R. Renslo, C. S. Craik
Broad-Spectrum Allosteric Inhibition Of Herpesvirus Proteases.
Biochemistry V. 53 4648 2014
PubMed-ID: 24977643  |  Reference-DOI: 10.1021/BI5003234

(-) Compounds

Molecule 1 - KSHV PROTEASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-194
    Organism Common: HHV-8
    Organism Scientific: HUMAN HERPESVIRUS 8
    Organism Taxid: 37296

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (2x): A (2x)B (2x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
124Q3Ligand/Ion6-(CYCLOHEXYLMETHYL)-N-[4-(METHYLSULFONYLCARBAMOYL)-2-(PHENYLMETHYL)PHENYL]PYRIDINE-2-CARBOXAMIDE
2DMS1Ligand/IonDIMETHYL SULFOXIDE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
124Q1Ligand/Ion6-(CYCLOHEXYLMETHYL)-N-[4-(METHYLSULFONYLCARBAMOYL)-2-(PHENYLMETHYL)PHENYL]PYRIDINE-2-CARBOXAMIDE
2DMS1Ligand/IonDIMETHYL SULFOXIDE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
124Q2Ligand/Ion6-(CYCLOHEXYLMETHYL)-N-[4-(METHYLSULFONYLCARBAMOYL)-2-(PHENYLMETHYL)PHENYL]PYRIDINE-2-CARBOXAMIDE
2DMS-1Ligand/IonDIMETHYL SULFOXIDE
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
124Q2Ligand/Ion6-(CYCLOHEXYLMETHYL)-N-[4-(METHYLSULFONYLCARBAMOYL)-2-(PHENYLMETHYL)PHENYL]PYRIDINE-2-CARBOXAMIDE
2DMS2Ligand/IonDIMETHYL SULFOXIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:76 , ILE A:105 , LEU A:110 , PHE A:189 , PRO A:192 , LEU A:193 , LEU A:196 , HOH A:303 , PRO B:192 , LEU B:193 , THR B:195 , 24Q B:201 , 24Q B:202binding site for residue 24Q A 201
2AC2SOFTWAREALA A:92 , ALA B:92 , PRO B:93binding site for residue DMS A 202
3AC3SOFTWARELYS A:18 , GLU A:45 , TRP A:109 , ALA A:139 , 24Q A:201 , HOH A:312 , LEU B:79 , ALA B:80 , LEU B:83 , VAL B:89 , ALA B:90 , ILE B:105 , TRP B:109 , SER B:191 , GLU B:194binding site for residue 24Q B 201
4AC4SOFTWAREARG A:82 , LEU A:83 , SER A:87 , TRP A:109 , 24Q A:201 , HOH A:308 , GLU B:45 , ALA B:139 , LEU B:140 , ARG B:144 , GLY B:145 , HOH B:309binding site for residue 24Q B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P2T)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gln A:3 -Gly A:4
2Leu A:34 -Pro A:35
3Leu B:34 -Pro B:35

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P2T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P2T)

(-) Exons   (0, 0)

(no "Exon" information available for 4P2T)

(-) 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:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.eeee.......eeehhhhhhhhh......eeee........eeeeeeee....eeeeeee.hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.eeeeee.hhhhh......eeeeeee..........eee.hhhhhhhh....hhhhhhhhhhhhh..hhhhh......hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4p2t A   3 QGLYVGGFVDVVSCPKLEQELYLDPDQVTDYLPVTEPLPITIEHLPETEVGWTLGLFQVSHGIFCTGAITSPAFLELASRLADTSHVARAPVKNLPKEPLLEILHTWLPGLSLSSIHPRELTPSGPVFQHVSLCALGRRRGTVAVYGHDAEWVVSRFSSVSKSERAHILQHVSSCRLEDLSTPNFVSPLETL 196
                                    12        22        32        42        52        62        72        82        92       102       112       122||     134       144       154       164       174       184       194  
                                                                                                                                                  123|                                                                      
                                                                                                                                                   126                                                                      


Chain B from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.eeee.......eeehhhhhhhhh......eeee........eeeeeeeee..eeeeeeee.hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.eeeeee.hhhhh.....eeeeeee..........eee.hhhhhhh.....hhhhhhhhhhhhhhhhhhhh......hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p2t B   4 GLYVGGFVDVVSCPKLEQELYLDPDQVTDYLPVTEPLPITIEHLPETEVGWTLGLFQVSHGIFCTGAITSPAFLELASRLADTSHVARAPVKNLPKEPLLEILHTWLPGLSLSSIHPRELPSGPVFQHVSLCALGRRRGTVAVYGHDAEWVVSRFSSVSKSERAHILQHVSSCRLEDLSTPNFVSPLETL 196
                                    13        23        33        43        53        63        73        83        93       103       113       123|      136       146       156       166       176       186       196
                                                                                                                                                 123|                                                                     
                                                                                                                                                  127
   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  (0, 0)

(no "SCOP Domain" information available for 4P2T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P2T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P2T)

(-) Gene Ontology  (8, 10)

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 Related Entries

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

UniProtKB/TrEMBL
        O36607_HHV8 | O36607: 1fl1 2pbk 4p3h

(-) Related Entries Specified in the PDB File

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