Structure of PDB 6x9b Chain B Binding Site BS02

Receptor Information
>6x9b Chain B (length=1214) Species: 707241 (Sinorhizobium meliloti SM11) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDA
AASTARKLIEALRGKSGVEGLVQEYSLSSQEGVALMCLAEALLRIPDTAT
RDALIRDKIADGNWKSHLRSLFVNAATWGLVVTGKLTSTVNDRSLAAALT
RLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGFSYS
YDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISIKLSAL
HPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDL
LEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLV
KGAYWDAEIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQ
FATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRP
CRIYAPVGTHETLLAYLVRRLLENGANSSFVHRINDPKVSIDELIADPVE
VVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEALRES
AAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARRAVRL
AADAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALNAI
AEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQIAA
ALVAGNPVLAKPAEETPLIAAEGVRILREAGIPASALQLLPGDGRVGAAL
VAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNAMIV
DSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDVADRILTMLKGALH
ELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLASETG
VGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATGYG
LTFGLHTRLDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSGTG
PKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEAEAA
RNAGSSSALGLDLELPGPVGERNLYTLHARGRILLVPATESGLYHQLAAA
LATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALVEGD
AERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVSASIN
TAAAGGNASLMAIG
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain6x9b Chain B Residue 2003 [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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PDB6x9b Structural analysis of prolines and hydroxyprolines binding to the l-glutamate-gamma-semialdehyde dehydrogenase active site of bifunctional proline utilization A.
Resolution1.46 Å
Binding residue
(original residue number in PDB)		I703 S704 P705 W706 N707 I712 K730 A732 E733 G763 G766 A767 T781 G782 S783 V786 I790 E810 T811 C844 E940 F942 F1010
Binding residue
(residue number reindexed from 1)		I684 S685 P686 W687 N688 I693 K711 A713 E714 G744 G747 A748 T762 G763 S764 V767 I771 E791 T792 C825 E921 F923 F991
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) N707 K730 E810 C844 E940 A1022
Catalytic site (residue number reindexed from 1) N688 K711 E791 C825 E921 A1003
Enzyme Commision number 1.2.1.88: L-glutamate gamma-semialdehyde dehydrogenase.
1.5.5.2: proline dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003677 DNA binding
GO:0003700 DNA-binding transcription factor activity
GO:0003842 1-pyrroline-5-carboxylate dehydrogenase activity
GO:0004657 proline dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
Biological Process
GO:0006355 regulation of DNA-templated transcription
GO:0006560 proline metabolic process
GO:0006561 proline biosynthetic process
GO:0006562 proline catabolic process
GO:0010133 proline catabolic process to glutamate
Cellular Component
GO:0009898 cytoplasmic side of plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6x9b, PDBe:6x9b, PDBj:6x9b
PDBsum6x9b
PubMed33333077
UniProtF7X6I3

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