SMTL ID : 5cpd.1

Methionine-alanine complex structure of peptide deformylase from Xanthomonas oryzae pv. oryzae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

3 x CD: CADMIUM ION(Non-covalent)

CD.1: 2 residues within 4Å: Chain A: M.1, E.37 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.37, A:E.37, H2O.3 CD.2: 5 residues within 4Å: Chain A: Q.51, C.99, H.141, H.145 Ligands: MET.8 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.141, A:H.145, H2O.1, H2O.1 CD.3: 2 residues within 4Å: Chain A: E.128, E.130 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.128, A:E.128, A:E.130, H2O.1, H2O.1

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

ACT.4: 6 residues within 4Å: Chain A: L.14, G.148, R.149, L.150, S.153 Ligands: NA.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.14 Hydrogen bonds: A:L.150, A:S.153 Water bridges: A:S.153 Salt bridges: A:R.149

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 3 residues within 4Å: Chain A: L.14, G.148 Ligands: ACT.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.14 NA.6: 2 residues within 4Å: Chain A: L.105, D.164 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.164 Water bridges: A:G.104

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 2 residues within 4Å: Chain A: N.22, E.27 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.22

1 x MET: METHIONINE(Non-covalent)

MET.8: 12 residues within 4Å: Chain A: G.44, V.45, G.46, Y.69, E.97, G.98, F.134, R.137, H.141, E.142 Ligands: CD.2, ALA.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.45 Hydrogen bonds: A:V.45, A:G.46, A:E.142

1 x ALA: ALANINE(Non-covalent)

ALA.9: 5 residues within 4Å: Chain A: R.68, Y.69, G.98, L.100 Ligands: MET.8 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:L.100 Hydrogen bonds: A:G.98, A:G.98, A.9 Water bridges: A:L.100 Salt bridges: A:R.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ngo, H.P.T. et al., Methionine-alanine complex structure of peptide deformylase from Xanthomonas oryzae pv. oryzae. To Be Published

Release Date

2016-08-03

Peptides

Peptide deformylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peptide deformylase

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