Structure of PDB 6s6x Chain A Binding Site BS01

Receptor Information

>6s6x Chain A (length=1472) Species: 192 (Azospirillum brasilense)

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 ID: FMN
• InChI: InChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
• InChIKey: FVTCRASFADXXNN-SCRDCRAPSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
  OpenEye OEToolkits 1.7.6: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
  ACDLabs 12.01: N=2C(=O)NC(=O)C3=Nc1cc(C)c(C)cc1N(C=23)CC(O)C(O)C(O)COP(=O)(O)O
  CACTVS 3.385: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C
  CACTVS 3.385: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C
• Formula: C17 H21 N4 O9 P
• Name: FLAVIN MONONUCLEOTIDE;
  RIBOFLAVIN MONOPHOSPHATE
• ChEMBL: CHEMBL1201794
• DrugBank: DB03247
• ZINC: ZINC000003831425
• PDB chain: 6s6x Chain A Residue 1501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6s6x Cryo-EM Structures of Azospirillum brasilense Glutamate Synthase in Its Oligomeric Assemblies.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): P856 G857 M858 E886 K999 G1029 T1030 G1071 G1072 I1092 G1093 T1094
• Binding residue (residue number reindexed from 1): P856 G857 M858 E886 K999 G1029 T1030 G1071 G1072 I1092 G1093 T1094
• Annotation score: 1

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

External links

• PDB: RCSB:6s6x, PDBe:6s6x, PDBj:6s6x
• PDBsum: 6s6x
• PubMed: 31473159
• UniProt: Q05755|GLTB_AZOBR Glutamate synthase [NADPH] large chain (Gene Name=gltB)