SMTL ID : 5cp0.1

MAS complex structure of peptide deformylase from Xanthomonas oryzae pv oryzae

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x MET- ALA- SER: MET-ALA-SER(Non-covalent)

MET-ALA-SER.1: 12 residues within 4Å: Chain A: H.43, G.44, V.45, G.46, S.66, P.70, E.97, G.98, F.134, H.141, E.142 Ligands: CD.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.45 Hydrogen bonds: A:H.43, A:V.45, A:G.46, A:S.66, A:G.98, A:E.142 Water bridges: A:H.43, A:Q.51, A:G.98

5 x CD: CADMIUM ION(Non-covalent)(Non-functional Binders)

CD.2: 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.2, H2O.4 CD.3: 1 residues within 4Å: Chain A: E.37 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.37, A:E.37 CD.4: 5 residues within 4Å: Chain A: Q.51, C.99, H.141, H.145 Ligands: MET-ALA-SER.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.99, A:H.141, A:H.145, H2O.1, H2O.8 CD.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CD.9: 3 residues within 4Å: Chain A: G.104, L.105, D.164 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.105, H2O.7

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

ACT.5: 5 residues within 4Å: Chain A: L.14, G.148, R.149, L.150, S.153 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 ACT.6: 3 residues within 4Å: Chain A: G.95, W.96, D.170 No protein-ligand interaction detected (PLIP) ACT.7: 3 residues within 4Å: Chain A: R.3, L.31, V.54 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.31 Salt bridges: A:R.3

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

NA.10: 1 residues within 4Å: Chain A: L.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ngo, H.P.T. et al., MAS 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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