SMTL ID : 4ffp.1

PylC in complex with L-lysine-Ne-D-ornithine (cocrystallized with L-lysine and D-ornithine)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x 0TF: N~6~-D-ornithyl-L-lysine(Non-covalent)

0TF.1: 17 residues within 4Å: Chain A: K.10, L.11, Q.12, E.72, S.137, S.169, E.171, D.225, E.227, R.243, P.245, S.246, Q.247, T.248, E.302 Ligands: PO4.3, ADP.6 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Q.12 Hydrogen bonds: A:L.11, A:Q.12, A:Q.12, A:E.72, A:E.72, A:S.169, A:S.169, A:R.243, A:R.243, A:S.246, A:S.246, A:E.302 Water bridges: A:K.10, A:G.13

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 23 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 Ligands: PO4.3, MG.4, MG.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.131, A:S.136, A:S.138, A:E.160, A:V.163 Salt bridges: A:K.104, A:K.104, A:K.131 pi-Stacking: A:F.129, A:F.129 ADP.6: 15 residues within 4Å: Chain A: G.8, G.9, K.10, D.31, K.32, N.33, F.48, D.49, V.50, I.51, N.71, E.72, N.73, C.76 Ligands: 0TF.1 10 PLIP interactions: 10 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 Water bridges: A:S.306 Salt bridges: A:K.10 pi-Cation interactions: A:K.32

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 10 residues within 4Å: Chain A: S.136, S.137, E.227, E.239, D.241, R.243 Ligands: 0TF.1, ADP.2, MG.4, MG.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.137, A:E.227 Water bridges: A:R.243 Salt bridges: A:R.243

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: E.227, E.239 Ligands: ADP.2, PO4.3, MG.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.227, A:E.239, H2O.7 MG.5: 6 residues within 4Å: Chain A: K.104, E.239, D.241 Ligands: ADP.2, PO4.3, MG.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.239, A:E.239, A:D.241, H2O.8

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

Putative uncharacterized protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Putative uncharacterized protein

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