Structure of PDB 6x99 Chain A Binding Site BS03

Receptor Information
>6x99 Chain A (length=1216) Species: 707241 (Sinorhizobium meliloti SM11) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDA
AASTARKLIEALRGKGSGVEGLVQEYSLSSQEGVALMCLAEALLRIPDTA
TRDALIRDKIADGNWKSHLSRSLFVNAATWGLVVTGKLTSTVNDRSLAAA
LTRLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGFS
YSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISIKLS
ALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSL
DLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVR
LVKGAYWDAEIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVF
PQFATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLD
RPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRINDPKVSIDELIADP
VEVVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEALR
ESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARRAV
RLAADAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALN
AIAEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQI
AAALVAGNPVLAKPAEETPLIAAEGVRILREAGIPASALQLLPGDGRVGA
ALVAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNAM
IVDSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDVADRILTMLKGA
LHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLASE
TGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATG
YGLTFGLHTRLDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSG
TGPKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEAE
AARNAGSSSALGLDLELPGPVGERNLYTLHARGRILLVPATESGLYHQLA
AALATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALVE
GDAERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVSAS
INTAAAGGNASLMAIG
Ligand information
Ligand IDDPR
InChIInChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m1/s1
InChIKeyONIBWKKTOPOVIA-SCSAIBSYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1C[C@@H](NC1)C(=O)O
CACTVS 3.370OC(=O)[CH]1CCCN1
OpenEye OEToolkits 1.7.0C1CC(NC1)C(=O)O
CACTVS 3.370OC(=O)[C@H]1CCCN1
ACDLabs 12.01O=C(O)C1NCCC1
FormulaC5 H9 N O2
NameD-PROLINE
ChEMBLCHEMBL80257
DrugBankDB02853
ZINCZINC000000895071
PDB chain6x99 Chain A Residue 2008 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6x99 Structural analysis of prolines and hydroxyprolines binding to the l-glutamate-gamma-semialdehyde dehydrogenase active site of bifunctional proline utilization A.
Resolution1.56 Å
Binding residue
(original residue number in PDB)		W574 T575 R744
Binding residue
(residue number reindexed from 1)		W557 T558 R727
Annotation score5
Binding affinityMOAD: Ki=1.5mM
Enzymatic activity
Catalytic site (original residue number in PDB) N707 K730 E810 C844 E940 A1022
Catalytic site (residue number reindexed from 1) N690 K713 E793 C827 E923 A1005
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:6x99, PDBe:6x99, PDBj:6x99
PDBsum6x99
PubMed33333077
UniProtF7X6I3

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