Structure of PDB 2vdc Chain F Binding Site BS01

Receptor Information
>2vdc Chain F (length=1472) Species: 192 (Azospirillum brasilense) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
CGVGFIAAIDGKPRRSVVEKGIEALKAVWHRGAVDADGKTGDGAGIHVAV
PQKFFKDHVKVIGHRAPDNKLAVGQVFLPRISLDAQEACRCIVETEILAF
GYYIYGWRQVPINVDIIGEKANATRPEIEQIIVGNNKGVSDEQFELDLYI
IRRRIEKAVKGEQINDFYICSLSARSIIYKGMFLAEQLTTFYPDLLDERF
ESDFAIYHQRYSTNTFPTWPLAQPFRMLAHNGEINTVKGNVNWMKAHETR
MEHPAFGTHMQDLKPVIGVGLSDSGSLDTVFEVMVRAGRTAPMVKMMLVP
QALTSSQTTPDNHKALIQYCNSVMEPWDGPAALAMTDGRWVVGGMDRNGL
RPMRYTITTDGLIIGGSETGMVKIDETQVIEKGRLGPGEMIAVDLQSGKL
YRDRELKDHLATLKPWDKWVQNTTHLDELVKTASLKGEPSDMDKAELRRR
QQAFGLTMEDMELILHPMVEDGKEAIGSMGDDSPIAVLSDKYRGLHHFFR
QNFSQVTNPPIDSLRERRVMSLKTRLGNLGNILDEDETQTRLLQLESPVL
TTAEFRAMRDYMGDTAAEIDATFPVDGGPEALRDALRRIRQETEDAVRGG
ATHVILTDEAMGPARAAIPAILATGAVHTHLIRSNLRTFTSLNVRTAEGL
DTHYFAVLIGVGATTVNAYLAQEAIAERHRRGLFGSMPLEKGMANYKKAI
DDGLLKIMSKMGISVISSYRGGGNFEAIGLSRALVAEHFPAMVSRISGIG
LNGIQKKVLEQHATAYNEEVVALPVGGFYRFRKSGDRHGWEGGVIHTLQQ
AVTNDSYTTFKKYSEQVNKRPPMQLRDLLELRSTKAPVPVDEVESITAIR
KRFITPGMSMGALSPEAHGTLNVAMNRIGAKSDSGEGGEDPARFRPDKNG
DNWNSAIKQVASGRFGVTAEYLNQCRELEIKVAQGAKPGEGGQLPGFKVT
EMIARLRHSTPGVMLISPPPHHDIYSIEDLAQLIYDLKQINPDAKVTVKL
VSRSGIGTIAAGVAKANADIILISGNSGGTGASPQTSIKFAGLPWEMGLS
EVHQVLTLNRLRHRVRLRTDGGLKTGRDIVIAAMLGAEEFGIGTASLIAM
GCIMVRQCHSNTCPVGVCVQDDKLRQKFVGTPEKVVNLFTFLAEEVREIL
AGLGFRSLNEVIGRTDLLHQVSRGAEHLDDLDLNPRLAQVDPGENARYCT
LQGRNEVPDTLDARIVADARPLFEEGEKMQLAYNARNTQRAIGTRLSSMV
TRKFGMFGLQPGHITIRLRGTAGQSLGAFAVQGIKLEVMGDANDYVGKGL
SGGTIVVRPTTSSPLETNKNTIIGNTVLYGATAGKLFAAGQAGERFAVRN
SGATVVVEGCGSNGCEYMTGGTAVILGRVGDNFAAGMTGGMAYVYDLDDS
LPLYINDESVIFQRIEVGHYESQLKHLIEEHVTETQSRFAAEILNDWARE
VTKFWQVVPKEMLNRLEVPVHL
Ligand information
Ligand IDOMT
InChIInChI=1S/C5H11NO4S/c1-11(9,10)3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m0/s1
InChIKeyUCUNFLYVYCGDHP-BYPYZUCNSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[S](=O)(=O)CC[CH](N)C(O)=O
ACDLabs 10.04O=S(=O)(C)CCC(C(=O)O)N
OpenEye OEToolkits 1.5.0CS(=O)(=O)CCC(C(=O)O)N
OpenEye OEToolkits 1.5.0CS(=O)(=O)CC[C@@H](C(=O)O)N
CACTVS 3.341C[S](=O)(=O)CC[C@H](N)C(O)=O
FormulaC5 H11 N O4 S
NameS-DIOXYMETHIONINE
ChEMBLCHEMBL442720
DrugBankDB03790
ZINCZINC000001691392
PDB chain2vdc Chain F Residue 2473 [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)		R210 N231 G232 E233 D273
Binding residue
(residue number reindexed from 1)		R210 N231 G232 E233 D273
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) C1 R31 Y211 N231 G232 M479 E886 Q934 K937 Q943
Catalytic site (residue number reindexed from 1) C1 R31 Y211 N231 G232 M479 E886 Q934 K937 Q943
Enzyme Commision number 1.4.1.13: glutamate synthase (NADPH).
Gene Ontology
Molecular Function
GO:0004355 glutamate synthase (NADPH) activity
GO:0015930 glutamate synthase activity
GO:0016491 oxidoreductase activity
GO:0016638 oxidoreductase activity, acting on the CH-NH2 group of donors
GO:0046872 metal ion binding
GO:0051538 3 iron, 4 sulfur cluster binding
Biological Process
GO:0006537 glutamate biosynthetic process
GO:0006541 glutamine metabolic process
GO:0019676 ammonia assimilation cycle
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
UniProtQ05755|GLTB_AZOBR Glutamate synthase [NADPH] large chain (Gene Name=gltB)

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