Structure of PDB 6x9d Chain B Binding Site BS01

Receptor Information
>6x9d Chain B (length=1217) Species: 707241 (Sinorhizobium meliloti SM11) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDA
AASTARKLIEALRGKHSGSGVEGLVQEYSLSSQEGVALMCLAEALLRIPD
TATRDALIRDKIADGNWKSHLRSLFVNAATWGLVVTGKLTSTVNDRSLAA
ALTRLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGF
SYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISIKL
SALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELS
LDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMV
RLVKGAYWDAEIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVV
FPQFATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKL
DRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRINDPKVSIDELIAD
PVEVVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEAL
RESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARRA
VRLAADAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSAL
NAIAEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQ
IAAALVAGNPVLAKPAEETPLIAAEGVRILREAGIPASALQLLPGDGRVG
AALVAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNA
MIVDSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDVADRILTMLKG
ALHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLAS
ETGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNAT
GYGLTFGLHTRLDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLS
GTGPKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEA
EAARNAGSSSALGLDLELPGPVGERNLYTLHARGRILLVPATESGLYHQL
AAALATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALV
EGDAERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVSA
SINTAAAGGNASLMAIG
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/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/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(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
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)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
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(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
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain6x9d Chain B Residue 2001 [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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PDB6x9d Structural analysis of prolines and hydroxyprolines binding to the l-glutamate-gamma-semialdehyde dehydrogenase active site of bifunctional proline utilization A.
Resolution1.54 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 E492 S498 F499
Binding residue
(residue number reindexed from 1)		D290 A291 V322 Q324 R351 V353 K354 G355 A356 Y357 W358 F376 T377 R378 K379 T382 A405 T406 H407 N408 Q431 C432 E476 S482 F483
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) N707 K730 E810 C844 E940 A1022
Catalytic site (residue number reindexed from 1) N691 K714 E794 C828 E924 A1006
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:6x9d, PDBe:6x9d, PDBj:6x9d
PDBsum6x9d
PubMed33333077
UniProtF7X6I3

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