Structure of PDB 6x9c Chain B Binding Site BS02

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 IDFDA
InChIInChI=1S/C27H35N9O15P2/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/h3-4,8-9,14-16,19-21,26,32,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H2,33,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyYPZRHBJKEMOYQH-UYBVJOGSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2NC3=C(NC(=O)NC3=O)N(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
CACTVS 3.341Cc1cc2NC3=C(NC(=O)NC3=O)N(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
ACDLabs 10.04O=C3C=2Nc1cc(c(cc1N(C=2NC(=O)N3)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)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
FormulaC27 H35 N9 O15 P2
NameDIHYDROFLAVINE-ADENINE DINUCLEOTIDE
ChEMBL
DrugBank
ZINCZINC000095099885
PDB chain6x9c Chain B Residue 1303 [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)		D306 A307 V338 Q340 R367 V369 K370 G371 A372 Y373 W374 F392 T393 R394 K395 T398 A421 T422 H423 N424 Q447 C448 Y473 E492 S498 F499
Binding residue
(residue number reindexed from 1)		D285 A286 V317 Q319 R346 V348 K349 G350 A351 Y352 W353 F371 T372 R373 K374 T377 A400 T401 H402 N403 Q426 C427 Y452 E471 S477 F478
Annotation score2
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

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

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