Structure of PDB 4q3a Chain D Binding Site BS03

Receptor Information

>4q3a Chain D (length=259) Species: 269797 (Methanosarcina barkeri str. Fusaro)

MALLTPDDLININMQLQKADSAVQEVTGLDIKGICKALYGTFSSSEKVGI
VPVTSGNGIIGNFSASLHAITQYFGFDSFVTDMPDVSGYYEAVQNGAEII
LMADDRTFLAHNLKNGKMANNQPCTGIIYAEIASRYLKADSKDVLVVGLG
KVGFPGAEHLVQKDFRVYGYDADETLLERATSNLGIIPFDPANPKKFSII
FEATPCANTIPEAVLSENCVLSTPGIPCAISEELRDKYEVQLIAEPLGIG
TASMLYSVL

Ligand information

• Ligand ID: 2YC
• InChI: InChI=1S/C12H21N3O3/c1-8-5-7-14-10(8)11(16)15-6-3-2-4-9(13)12(17)18/h7-10H,2-6,13H2,1H3,(H,15,16)(H,17,18)/t8-,9-,10-/m0/s1
• InChIKey: ZFOMKMMPBOQKMC-GUBZILKMSA-N
• SMILES:
  ACDLabs 12.01: O=C(NCCCCC(C(=O)O)N)C1N=CCC1C
  OpenEye OEToolkits 1.7.6: C[C@H]1CC=N[C@@H]1C(=O)NCCCC[C@@H](C(=O)O)N
  OpenEye OEToolkits 1.7.6: CC1CC=NC1C(=O)NCCCCC(C(=O)O)N
  CACTVS 3.385: C[CH]1CC=N[CH]1C(=O)NCCCC[CH](N)C(O)=O
  CACTVS 3.385: C[C@H]1CC=N[C@@H]1C(=O)NCCCC[C@H](N)C(O)=O
• Formula: C12 H21 N3 O3
• Name: N~6~-{[(2S,3S)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl}-L-lysine
• ZINC: ZINC000050875538
• PDB chain: 4q3a Chain D Residue 904

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4q3a The Formation of Pyrroline and Tetrahydropyridine Rings in Amino Acids Catalyzed by Pyrrolysine Synthase (PylD).
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): L3 L4 V53 G58 I59 I60 F63 A103 N121
• Binding residue (residue number reindexed from 1): L3 L4 V53 G58 I59 I60 F63 A103 N121
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 1.4.1.-

Gene Ontology

Molecular Function

• GO:0016491 oxidoreductase activity

Biological Process

• GO:0008652 amino acid biosynthetic process

External links

• PDB: RCSB:4q3a, PDBe:4q3a, PDBj:4q3a
• PDBsum: 4q3a
• PubMed: 24916332
• UniProt: Q46E80|PYLD_METBF Pyrrolysine synthase (Gene Name=pylD)