Structure of PDB 2vdc Chain I Binding Site BS02

Receptor Information
>2vdc Chain I (length=456) Species: 192 (Azospirillum brasilense) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QDFAEIYARFSDERANEQANRCSQCGVPFCQVHCPVSNNIPDWLKLTSEG
RLEEAYEVSQATNNFPEICGRICPQDRLCEGNCVIEQSTHGAVTIGSVEK
YINDTAWDQGWVKPRTPSRELGLSVGVIGAGPAGLAAAEELRAKGYEVHV
YDRYDRMGGLLVYGIPGFKLEKSVVERRVKLLADAGVIYHPNFEVGRDAS
LPELRRKHVAVLVATGVYKARDIKAPGSGLGNIVAALDYLTTSNKVSLGD
TVEAYENGSLNAAGKHVVVLGGGDTAMDCVRTAIRQGATSVKCLYRRDRK
NMPGSQREVAHAEEEGVEFIWQAAPEGFTGDTVVTGVRAVRIHLGVADAT
GRQTPQVIEGSEFTVQADLVIKALGFEPEDLPNAFDEPELKVTRWGTLLV
DHRTKMTNMDGVFAAGDIVRGASLVVWAIRDGRDAAEGIHAYAKAKAEAP
VAVAAE
Ligand information
Ligand IDSF4
InChIInChI=1S/4Fe.4S
InChIKeyLJBDFODJNLIPKO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7[S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
CACTVS 3.385S1[Fe]S[Fe]1.S2[Fe]S[Fe]2
FormulaFe4 S4
NameIRON/SULFUR CLUSTER
ChEMBL
DrugBank
ZINC
PDB chain2vdc Chain I Residue 483 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2vdc The Subnanometer Resolution Structure of the Glutamate Synthase 1.2-Mda Hexamer by Cryoelectron Microscopy and its Oligomerization Behavior in Solution: Functional Implications.
Resolution9.5 Å
Binding residue
(original residue number in PDB)		C47 S48 Q49 C50 C55 C108 V109 V118 I120
Binding residue
(residue number reindexed from 1)		C22 S23 Q24 C25 C30 C83 V84 V93 I95
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) F193 D303
Catalytic site (residue number reindexed from 1) F168 D278
Enzyme Commision number 1.4.1.13: glutamate synthase (NADPH).
Gene Ontology
Molecular Function
GO:0004355 glutamate synthase (NADPH) activity
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0051536 iron-sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0006537 glutamate biosynthetic process
GO:0097054 L-glutamate biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2vdc, PDBe:2vdc, PDBj:2vdc
PDBsum2vdc
PubMed18199747
UniProtQ05756|GLTD_AZOBR Glutamate synthase [NADPH] small chain (Gene Name=gltD)

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