Structure of PDB 6x9c Chain B Binding Site BS01

Receptor Information
>6x9c Chain B (length=1208) Species: 707241 (Sinorhizobium meliloti SM11) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAA
ASTARKLIEALRGKSGVEGLVQEYSLSSQEGVALMCLAEALLRIPDTATR
DALIRDKIADGNWKSHLRSLFVNAATWGLVVTGKLTSTVNDRSLAAALTR
LISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGFSYSY
DMLEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISIKLSALHP
RYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLE
VLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKG
AYWDAEIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFA
THNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRPCR
IYAPVGTHETLLAYLVRRLLENGANSSFVHRINDPKVSIDELIADPVEVV
RAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEALRESAA
MKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARRAVRLAA
DAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALNAIAE
VREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQIAAAL
VAGNPVLAKPAEETPLIAAEGVRILREAGIPASALQLLPGDGRVGAALVA
AAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNAMIVDS
SALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDVADRILTMLKGALHEL
HIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLASETGVG
TFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATGYGLT
FGLHTRLDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSGTGPK
AGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEAEAARN
AGSSSALGLDLELPGPVGERNLYTLHARGRILLVPATESGLYHQLAAALA
TGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALVEGDAE
RIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVSASINTA
AAGGNASL
Ligand information
Ligand IDNAI
InChIInChI=1S/C21H29N7O14P2/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/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBOPGDPNILDQYTO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[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 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[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
FormulaC21 H29 N7 O14 P2
Name1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE;
NADH
ChEMBLCHEMBL1234616
DrugBankDB00157
ZINCZINC000008215403
PDB chain6x9c Chain B Residue 1301 [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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PDB6x9c Structural analysis of prolines and hydroxyprolines binding to the l-glutamate-gamma-semialdehyde dehydrogenase active site of bifunctional proline utilization A.
Resolution1.44 Å
Binding residue
(original residue number in PDB)		I703 S704 P705 W706 N707 K730 E733 G763 G766 A767 F780 G782 S783 V786 I790 C844 E940 F942
Binding residue
(residue number reindexed from 1)		I682 S683 P684 W685 N686 K709 E712 G742 G745 A746 F759 G761 S762 V765 I769 C823 E919 F921
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) N707 K730 E810 C844 E940 A1022
Catalytic site (residue number reindexed from 1) N686 K709 E789 C823 E919 A1001
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

View graph for
Molecular Function
View graph for
Biological Process
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Cellular Component
External links
PDB RCSB:6x9c, PDBe:6x9c, PDBj:6x9c
PDBsum6x9c
PubMed33333077
UniProtF7X6I3

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