Structure of PDB 2vdc Chain I Binding Site BS03

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 IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain2vdc Chain I Residue 484 [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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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)		I97 I153 G154 G156 P157 A158 R178 G184 L185 I190 E219 V220 A239 T240 D299 T300 D442 L449 V450
Binding residue
(residue number reindexed from 1)		I72 I128 G129 G131 P132 A133 R153 G159 L160 I165 E194 V195 A214 T215 D274 T275 D417 L424 V425
Annotation score2
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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