SMTL ID : 5jez.1

Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with tripeptide Met-Ala-Ser

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x MET- ALA- SER: Met-Ala-Ser(Non-covalent)

MET-ALA-SER.1: 13 residues within 4Å: Chain A: G.69, G.70, V.71, G.72, L.125, E.129, G.130, L.132, Y.167, V.171, H.174, E.175 Ligands: ZN.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.69, A:V.71, A:G.72, A:G.130 Water bridges: A:G.69, A:L.132

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 5 residues within 4Å: Chain A: H.145, Q.173, D.177, R.187 Ligands: ZN.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.173 Water bridges: A:Q.173, A:R.187 Salt bridges: A:H.145, A:R.187

8 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: Q.77, C.131, H.174, H.178 Ligands: MET-ALA-SER.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.174, A:H.178, H2O.2, H2O.9 ZN.4: 1 residues within 4Å: Chain A: H.55 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.55, H2O.10 ZN.5: 1 residues within 4Å: Chain A: H.118 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.118, H2O.9, H2O.9, H2O.10 ZN.6: 1 residues within 4Å: Chain A: E.190 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.190, A:E.190, H2O.4 ZN.7: 2 residues within 4Å: Chain A: H.145 Ligands: ACT.2 3 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:H.145, ACT.2, H2O.9 ZN.8: 4 residues within 4Å: Chain A: H.12, L.13, D.15, D.18 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.18, A:D.18, H2O.1, H2O.1, H2O.9 ZN.9: 2 residues within 4Å: Chain A: E.43, E.47 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.43, A:E.47, H2O.5 ZN.10: 3 residues within 4Å: Chain A: E.151, K.159, R.161 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.151, A:E.151, H2O.9, H2O.10, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fieulaine, S. et al., A unique peptide deformylase platform to rationally design and challenge novel active compounds. Sci Rep (2016)

Release Date

2016-11-30

Peptides

Peptide deformylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peptide deformylase

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