Structure of PDB 4ffo Chain A Binding Site BS01

Receptor Information
>4ffo Chain A (length=353) Species: 269797 (Methanosarcina barkeri str. Fusaro) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKTICLVGGKLQGFEAAYLSKKAGMKVVLVDKNPQALIRNYADEFYCFDV
IKEPEKLLELSKRVDAVLPVNENLACIEFLNSIKEKFSCPVLFDFEAYRI
SRDKKKSKDYFKSIGVPTPQDRPSKPPYFVKPPCESSSVGARIIYGLEPD
TLVEEYVEGEVVSLEVVGDGSHFAVVKETLVHIDETYDCHMVTPLPANPL
FRQISHDLAANLPLKGIMDVEAIFGPKGLRVIEIDARFPSQTPTVVYYSS
GINLIELLFRAFTDGVEEIENKYCIYEHLMFGENGVLIPVGEQVLSMGSD
YGKFYEEPGIEIFLCKGEYPVFTMVFWGKDREETGAKRCKGLSVLKERFG
AVL
Ligand information
Ligand ID0TK
InChIInChI=1S/C5H13N2O5P/c6-3-1-2-4(7)5(8)12-13(9,10)11/h4H,1-3,6-7H2,(H2,9,10,11)/t4-/m1/s1
InChIKeyMNDHJWIHMSHXOW-SCSAIBSYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370NCCC[C@@H](N)C(=O)O[P](O)(O)=O
OpenEye OEToolkits 1.7.6C(CC(C(=O)OP(=O)(O)O)N)CN
CACTVS 3.370NCCC[CH](N)C(=O)O[P](O)(O)=O
OpenEye OEToolkits 1.7.6C(C[C@H](C(=O)OP(=O)(O)O)N)CN
ACDLabs 12.01O=P(OC(=O)C(N)CCCN)(O)O
FormulaC5 H13 N2 O5 P
Name(2R)-2,5-diaminopentanoyl dihydrogen phosphate;
phosphorylated D-ornithine
ChEMBL
DrugBank
ZINCZINC000098207867
PDB chain4ffo Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ffo Biosynthesis of the 22nd genetically encoded amino acid pyrrolysine: structure and reaction mechanism of PylC at 1.5A resolution.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		S137 S169 D225 E227 E239 D241 R243 S246 T248 E302
Binding residue
(residue number reindexed from 1)		S137 S163 D219 E221 E233 D235 R237 S240 T242 E292
Annotation score2
Enzymatic activity
Enzyme Commision number 6.3.2.59: 3-methyl-D-ornithine--L-lysine ligase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0008652 amino acid biosynthetic process
GO:0071524 pyrrolysine biosynthetic process
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4ffo, PDBe:4ffo, PDBj:4ffo
PDBsum4ffo
PubMed22985965
UniProtQ46E79|PYLC_METBF 3-methyl-D-ornithine--L-lysine ligase (Gene Name=pylC)

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