Structure of PDB 6x9c Chain B Binding Site BS03

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 IDPRO
InChIInChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1
InChIKeyONIBWKKTOPOVIA-BYPYZUCNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1C[C@H](NC1)C(=O)O
CACTVS 3.341OC(=O)[C@@H]1CCCN1
CACTVS 3.341OC(=O)[CH]1CCCN1
OpenEye OEToolkits 1.5.0C1CC(NC1)C(=O)O
ACDLabs 10.04O=C(O)C1NCCC1
FormulaC5 H9 N O2
NamePROLINE
ChEMBLCHEMBL54922
DrugBankDB00172
ZINCZINC000000895360
PDB chain6x9c Chain B Residue 1307 [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)		E674 F708 C844 S845 G1002 A1003 F1010
Binding residue
(residue number reindexed from 1)		E653 F687 C823 S824 G981 A982 F989
Annotation score5
Binding affinityMOAD: Ki=11mM
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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