Structure of PDB 2vgr Chain D Binding Site BS01

Receptor Information
>2vgr Chain D (length=213) Species: 268746 (Prochlorococcus phage P-SSM2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KTIWQNYIDALFETFPQLEISEVWAKWDGGNVTKDGGDAKLTANIRTGEH
FLKAREAHIVDPNSDIYNTILYPKTGADLPCFGMDLMKFSDKKVIIVFDF
QHPREKYLFSVDGLPEDDGKYRFFEMGNHFSKNIFVRYCKPDEVDQYLDT
FKLYLTKYKEMIDNNKPVGEDTTVYSDFDTYMTELDPVRGYMKNKFGEGR
SEAFVNDFLFSYK
Ligand information
Ligand IDBLA
InChIInChI=1S/C33H34N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h7-8,13-15,34H,1-2,9-12H2,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b26-13-,27-14-,29-15-
InChIKeyGWZYPXHJIZCRAJ-SRVCBVSDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1c(c([nH]c1\C=C/2\C(=C(C(=O)N2)C=C)C)\C=C/3\C(=C(C(=N3)\C=C/4\C(=C(C(=O)N4)C)C=C)C)CCC(=O)O)CCC(=O)O
OpenEye OEToolkits 1.5.0Cc1c(c([nH]c1C=C2C(=C(C(=O)N2)C=C)C)C=C3C(=C(C(=N3)C=C4C(=C(C(=O)N4)C)C=C)C)CCC(=O)O)CCC(=O)O
CACTVS 3.341Cc1c([nH]c(C=C2N=C(C=C3NC(=O)C(=C3C=C)C)C(=C2CCC(O)=O)C)c1CCC(O)=O)C=C4NC(=O)C(=C4C)C=C
CACTVS 3.341Cc1c([nH]c(\C=C2/N=C(\C=C3/NC(=O)C(=C3C=C)C)C(=C2CCC(O)=O)C)c1CCC(O)=O)\C=C4/NC(=O)C(=C4C)C=C
FormulaC33 H34 N4 O6
NameBILIVERDINE IX ALPHA
ChEMBL
DrugBank
ZINCZINC000103534374
PDB chain2vgr Chain D Residue 1234 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2vgr Phycoerythrobilin Synthase (Pebs) of a Marine Virus: Crystal Structures of the Biliverdin Complex and the Substrate-Free Form.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		I86 N88 I90 G103 M104 D105 M107 F109 V117 Q121 R142 F143 V156 Y158 M202 V208 Y211
Binding residue
(residue number reindexed from 1)		I66 N68 I70 G83 M84 D85 M87 F89 V97 Q101 R122 F123 V136 Y138 M182 V188 Y191
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) D105 D206
Catalytic site (residue number reindexed from 1) D85 D186
Enzyme Commision number 1.3.7.6: phycoerythrobilin synthase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0016636 oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor
GO:0050897 cobalt ion binding
Biological Process
GO:0010024 phytochromobilin biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2vgr, PDBe:2vgr, PDBj:2vgr
PDBsum2vgr
PubMed18662988
UniProtQ58MU6|PEBS_BPPRM Phycoerythrobilin synthase (Gene Name=pebS)

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