SMTL ID : 4ffl.1

PylC in complex with L-lysine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x LYS: LYSINE(Non-covalent)

LYS.1: 11 residues within 4Å: Chain A: K.10, L.11, Q.12, E.72, S.136, S.137, R.243, S.246, E.302 Ligands: PO4.3, ATP.8 10 PLIP interactions: 1 Ligand-Ligand interactions, 9 interactions with chain A Hydrogen bonds: K.1, A:L.11, A:Q.12, A:Q.12, A:E.72, A:E.72 Hydrophobic interactions: A:Q.12 Water bridges: A:G.13, A:S.246, A:S.246

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

ADP.2: 22 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 Ligands: PO4.3, MG.4, MG.5 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:K.131, A:S.136, A:S.137, A:S.138, A:E.160, A:V.163, A:E.227 Water bridges: A:S.138, A:S.138 Salt bridges: A:K.104, A:K.104, A:K.131 pi-Stacking: A:F.129, A:F.129

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

PO4.3: 12 residues within 4Å: Chain A: S.136, S.137, E.227, E.239, D.241, R.243 Ligands: LYS.1, ADP.2, MG.4, MG.5, MG.6, CO3.7 9 PLIP interactions: 2 Ligand-Ligand interactions, 7 interactions with chain A Water bridges: K.1, A:R.243, A:R.243, A:R.243, A:E.302 Salt bridges: K.1, A:R.243 Hydrogen bonds: A:S.137, A:E.227

3 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: E.227, E.239 Ligands: ADP.2, PO4.3, MG.5, MG.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.227, A:E.239, H2O.11 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.11 MG.6: 6 residues within 4Å: Chain A: D.225, E.227, E.239 Ligands: PO4.3, MG.4, CO3.7 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.227, H2O.10, H2O.11

1 x CO3: CARBONATE ION(Non-functional Binders)

CO3.7: 6 residues within 4Å: Chain A: V.187, E.227, S.246, Q.247 Ligands: PO4.3, MG.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.247 Water bridges: A:S.246

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

ATP.8: 14 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 Ligands: LYS.1 16 PLIP interactions: 2 Ligand-Ligand interactions, 14 interactions with chain A Hydrogen bonds: K.1, A:G.9, A:K.32, A:K.32, A:D.49, A:V.50, A:E.72, A:N.73 Water bridges: K.1, A:N.33, A:N.33, A:N.33, A:E.72 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

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