SMTL ID : 4ffn.1

PylC in complex with D-ornithine and AMPPNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x ORD: D-ORNITHINE(Non-covalent)

ORD.1: 11 residues within 4Å: Chain A: S.169, E.171, D.225, E.227, R.243, P.245, S.246, Q.247, T.248, E.302 Ligands: ANP.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.248 Hydrogen bonds: A:S.169, A:S.246, A:Q.247, A:T.248 Salt bridges: A:R.243

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.2: 24 residues within 4Å: Chain A: K.104, P.119, F.129, K.131, E.135, S.136, S.137, S.138, E.160, E.161, Y.162, V.163, V.167, I.189, Y.193, E.227, I.229, I.238, E.239, D.241, R.243 Ligands: ORD.1, MG.3, MG.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:K.104, A:K.131, A:E.135, A:S.137, A:S.138, A:E.161, A:V.163, A:R.243 Water bridges: A:S.138, A:Y.193 Salt bridges: A:K.104, A:K.131 pi-Stacking: A:F.129, A:F.129

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: E.227, E.239 Ligands: ANP.2, MG.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.227, A:E.239, H2O.6 MG.4: 6 residues within 4Å: Chain A: K.104, E.227, E.239, D.241 Ligands: ANP.2, MG.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.239, A:E.239, A:D.241

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.5: 13 residues within 4Å: Chain A: G.8, G.9, K.10, D.31, K.32, F.48, D.49, V.50, I.51, N.71, E.72, N.73, C.76 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.9, A:K.32, A:K.32, A:D.49, A:V.50, A:E.72, A:N.73, A:N.73 Salt bridges: A:K.10, A:K.10 pi-Cation interactions: A:K.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Quitterer, F. et al., Biosynthesis of the 22nd genetically encoded amino acid pyrrolysine: structure and reaction mechanism of PylC at 1.5A resolution. J.Mol.Biol. (2012)

Release Date

2012-09-19

Peptides

PylC: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PylC

Related Entries With Identical Sequence