Structure of PDB 6x9d Chain A Binding Site BS02

Receptor Information
>6x9d Chain A (length=1218) Species: 707241 (Sinorhizobium meliloti SM11) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDA
AASTARKLIEALRGKHSGSGVEGLVQEYSLSSQEGVALMCLAEALLRIPD
TATRDALIRDKIADGNWKSHLSRSLFVNAATWGLVVTGKLTSTVNDRSLA
AALTRLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKG
FSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISIK
LSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLEL
SLDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIM
VRLVKGAYWDAEIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDV
VFPQFATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGK
LDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRINDPKVSIDELIA
DPVEVVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEA
LRESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARR
AVRLAADAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSA
LNAIAEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTG
QIAAALVAGNPVLAKPAEETPLIAAEGVRILREAGIPASALQLLPGDGRV
GAALVAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQN
AMIVDSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDVADRILTMLK
GALHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLA
SETGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNA
TGYGLTFGLHTRLDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGL
SGTGPKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAE
AEAARNAGSSSALGLDLELPGPVGERNLYTLHARGRILLVPATESGLYHQ
LAAALATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGAL
VEGDAERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVS
ASINTAAAGGNASLMAIG
Ligand information
Ligand IDHYP
InChIInChI=1S/C5H9NO3/c7-3-1-4(5(8)9)6-2-3/h3-4,6-7H,1-2H2,(H,8,9)/t3-,4+/m1/s1
InChIKeyPMMYEEVYMWASQN-DMTCNVIQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1C(CNC1C(=O)O)O
OpenEye OEToolkits 1.5.0C1[C@H](CN[C@@H]1C(=O)O)O
CACTVS 3.341O[CH]1CN[CH](C1)C(O)=O
CACTVS 3.341O[C@H]1CN[C@@H](C1)C(O)=O
ACDLabs 10.04O=C(O)C1NCC(O)C1
FormulaC5 H9 N O3
Name4-HYDROXYPROLINE;
HYDROXYPROLINE
ChEMBLCHEMBL352418
DrugBankDB08847
ZINCZINC000000901791
PDB chain6x9d Chain A Residue 2002 [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)		E674 F708 I712 R843 S845 G1002 A1003 F1010
Binding residue
(residue number reindexed from 1)		E659 F693 I697 R828 S830 G987 A988 F995
Annotation score2
Binding affinityMOAD: Ki=7mM
Enzymatic activity
Catalytic site (original residue number in PDB) N707 K730 E810 C844 E940 A1022
Catalytic site (residue number reindexed from 1) N692 K715 E795 C829 E925 A1007
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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