Structure of PDB 2ybq Chain A Binding Site BS01

Receptor Information
>2ybq Chain A (length=242) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VDFPAGSVALVGAGPGDPGLLTLRAWALLQQAEVVVYDRLVARELIALLP
ESCQRIYVGPQEEINELLVRLARQQRRVVRLKGGDPFIFGRGAEELERLL
EAGVDCQVVPGVTAASGCSTYAGIPLTHRDLAQSCTFVTGHLQLDLDWAG
LARGKQTLVFYMGLGNLAEIAARLVEHGLASDTPAALVSQGTQAGQQVTR
GALAELPALARRYQLKPPTLIVVGQVVALFAERAMAHPSYLG
Ligand information
Ligand IDSAH
InChIInChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
InChIKeyZJUKTBDSGOFHSH-WFMPWKQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
CACTVS 3.341N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
FormulaC14 H20 N6 O5 S
NameS-ADENOSYL-L-HOMOCYSTEINE
ChEMBLCHEMBL418052
DrugBankDB01752
ZINCZINC000004228232
PDB chain2ybq Chain A Residue 1267 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2ybq Crystal Structure of the Heme D1 Biosynthesis Enzyme Nire in Complex with its Substrate Reveals New Insights Into the Catalytic Mechanism of S-Adenosyl-L-Methionine-Dependent Uroporphyrinogen III Methyltransferases.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		L52 G103 G104 D105 I108 F109 T133 A134 C138 Y185 M186 G215 P242 T243 L244
Binding residue
(residue number reindexed from 1)		L40 G83 G84 D85 I88 F89 T113 A114 C118 Y161 M162 G191 P218 T219 L220
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) D50 M186
Catalytic site (residue number reindexed from 1) D38 M162
Enzyme Commision number 2.1.1.107: uroporphyrinogen-III C-methyltransferase.
Gene Ontology
Molecular Function
GO:0004851 uroporphyrin-III C-methyltransferase activity
GO:0008168 methyltransferase activity
Biological Process
GO:0006779 porphyrin-containing compound biosynthetic process
GO:0009236 cobalamin biosynthetic process
GO:0019354 siroheme biosynthetic process
GO:0032259 methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2ybq, PDBe:2ybq, PDBj:2ybq
PDBsum2ybq
PubMed21632530
UniProtP95417

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