Structure of PDB 4ffm Chain A Binding Site BS01

Receptor Information
>4ffm Chain A (length=344) 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
SRDKKKSKDYFKSIGVPTPQDRPSKPPYFVKARIIYGLEPDTLVEEYVEG
EVVSLEVVGDGSHFAVVKETLVHIDETYDCHMVTPLPANPLFRQISHDLA
ANLPLKGIMDVEAIFGPKGLRVIEIDARFPSQTPTVVYYSSGINLIELLF
RAFTDGVEEIENKYCIYEHLMFGENGVLIPVGEQVLSMGSDYGKFYEEPG
IEIFLCKGEYPVFTMVFWGKDREETGAKRCKGLSVLKERFGAVL
Ligand information
Ligand ID0TF
InChIInChI=1S/C11H24N4O3/c12-6-3-5-8(13)10(16)15-7-2-1-4-9(14)11(17)18/h8-9H,1-7,12-14H2,(H,15,16)(H,17,18)/t8-,9+/m1/s1
InChIKeyAOOVWOOUTNDWMA-BDAKNGLRSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)C(N)CCCCNC(=O)C(N)CCCN
OpenEye OEToolkits 1.7.6C(CCNC(=O)[C@@H](CCCN)N)C[C@@H](C(=O)O)N
CACTVS 3.370NCCC[C@@H](N)C(=O)NCCCC[C@H](N)C(O)=O
CACTVS 3.370NCCC[CH](N)C(=O)NCCCC[CH](N)C(O)=O
OpenEye OEToolkits 1.7.6C(CCNC(=O)C(CCCN)N)CC(C(=O)O)N
FormulaC11 H24 N4 O3
NameN~6~-D-ornithyl-L-lysine
ChEMBL
DrugBank
ZINCZINC000095920521
PDB chain4ffm 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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PDB4ffm Biosynthesis of the 22nd genetically encoded amino acid pyrrolysine: structure and reaction mechanism of PylC at 1.5A resolution.
Resolution1.91 Å
Binding residue
(original residue number in PDB)		K10 L11 Q12 E72 S169 D225 P245 S246 Q247 T248 E302
Binding residue
(residue number reindexed from 1)		K10 L11 Q12 E72 S154 D210 P230 S231 Q232 T233 E283
Annotation score3
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:4ffm, PDBe:4ffm, PDBj:4ffm
PDBsum4ffm
PubMed22985965
UniProtQ46E79|PYLC_METBF 3-methyl-D-ornithine--L-lysine ligase (Gene Name=pylC)

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