Structure of PDB 6x9a Chain A Binding Site BS02

Receptor Information
>6x9a Chain A (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
AASTARKLIEALRGKGVEGLVQEYSLSSQEGVALMCLAEALLRIPDTATR
DALIRDKIADGNWKSHLSRSLFVNAATWGLVVTGKLTSTVNDRSLAAALT
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 IDUY7
InChIInChI=1S/C5H9NO3/c7-3-1-4(5(8)9)6-2-3/h3-4,6-7H,1-2H2,(H,8,9)/t3-,4+/m0/s1
InChIKeyPMMYEEVYMWASQN-IUYQGCFVSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C1C(O)CNC1C(O)=O
OpenEye OEToolkits 2.0.7C1C(CNC1C(=O)O)O
CACTVS 3.385O[CH]1CN[CH](C1)C(O)=O
OpenEye OEToolkits 2.0.7C1[C@@H](CN[C@H]1C(=O)O)O
CACTVS 3.385O[C@@H]1CN[C@H](C1)C(O)=O
FormulaC5 H9 N O3
Name(4S)-4-hydroxy-D-proline
ChEMBL
DrugBank
ZINCZINC000000895457
PDB chain6x9a Chain A Residue 2004 [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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PDB6x9a Structural analysis of prolines and hydroxyprolines binding to the l-glutamate-gamma-semialdehyde dehydrogenase active site of bifunctional proline utilization A.
Resolution1.41 Å
Binding residue
(original residue number in PDB)		E674 F708 S845 G1002 A1003 F1010
Binding residue
(residue number reindexed from 1)		E655 F689 S826 G983 A984 F991
Annotation score2
Binding affinityMOAD: Ki=4.5mM
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:6x9a, PDBe:6x9a, PDBj:6x9a
PDBsum6x9a
PubMed33333077
UniProtF7X6I3

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