Structure of PDB 4ffp Chain A Binding Site BS01

Receptor Information
>4ffp 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 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 chain4ffp Chain A Residue 901 [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]
PDB4ffp 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)		K10 L11 Q12 E72 S169 D225 R243 P245 S246 Q247 T248 E302
Binding residue
(residue number reindexed from 1)		K10 L11 Q12 E72 S163 D219 R237 P239 S240 Q241 T242 E292
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4ffp, PDBe:4ffp, PDBj:4ffp
PDBsum4ffp
PubMed22985965
UniProtQ46E79|PYLC_METBF 3-methyl-D-ornithine--L-lysine ligase (Gene Name=pylC)

[Back to BioLiP]