Structure of PDB 2ybo Chain A Binding Site BS01

Receptor Information
>2ybo Chain A (length=248) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LDVDFPAGSVALVGAGPGDPGLLTLRAWALLQQAEVVVYDRLVARELIAL
LPESCQRIYVGPQEEINELLVRLARQQRRVVRLKGGDPFIFGRGAEELER
LLEAGVDCQVVPGVTAASGCSTYAGIPLTHRDLAQSCTFVTGHLQNDGRL
DLDWAGLARGKQTLVFYMGLGNLAEIAARLVEHGLASDTPAALVSQGTQA
GQQVTRGALAELPALARRYQLKPPTLIVVGQVVALFAERAMAHPSYLG
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 chain2ybo Chain A Residue 1267 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2ybo 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 Q214 G215 P242 T243
Binding residue
(residue number reindexed from 1)		L42 G85 G86 D87 I90 F91 T115 A116 C120 Y167 M168 Q196 G197 P224 T225
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) D50 M186
Catalytic site (residue number reindexed from 1) D40 M168
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:2ybo, PDBe:2ybo, PDBj:2ybo
PDBsum2ybo
PubMed21632530
UniProtP95417

[Back to BioLiP]