SMTL ID : 4nt8.1

Formyl-methionine-alanine complex structure of peptide deformylase from Xanthomoonas oryzae pv. oryzae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

6 x CD: CADMIUM ION(Non-covalent)

CD.1: 2 residues within 4Å: Chain A: M.1, E.37 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.37, A:E.37, H2O.3, H2O.3, H2O.3 CD.2: 5 residues within 4Å: Chain A: Q.51, C.99, H.141, H.145 Ligands: FME.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.141, A:H.145, H2O.3 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.3, H2O.3 CD.10: 2 residues within 4Å: Chain B: M.1, E.37 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.37, B:E.37, H2O.7, H2O.7, H2O.7 CD.11: 5 residues within 4Å: Chain B: Q.51, C.99, H.141, H.145 Ligands: FME.16 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.141, B:H.145, H2O.7 CD.12: 2 residues within 4Å: Chain B: E.128, E.130 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.128, B:E.128, B:E.130, H2O.7, H2O.7

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

ACT.4: 7 residues within 4Å: Chain A: L.14, G.148, R.149, L.150, S.153 Chain B: F.158, D.159 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.14 Hydrogen bonds: A:L.150, A:L.150, A:S.153 Water bridges: A:R.149, A:S.153 Salt bridges: A:R.149 ACT.13: 7 residues within 4Å: Chain A: F.158, D.159 Chain B: L.14, G.148, R.149, L.150, S.153 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.14 Hydrogen bonds: B:L.150, B:L.150, B:S.153 Water bridges: B:R.149, B:S.153 Salt bridges: B:R.149

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

NA.5: 3 residues within 4Å: Chain A: L.14, G.148 Chain B: D.159 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.148 NA.6: 2 residues within 4Å: Chain A: L.105, D.164 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.105 NA.14: 3 residues within 4Å: Chain A: D.159 Chain B: L.14, G.148 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.14 NA.15: 2 residues within 4Å: Chain B: L.105, D.164 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.164

2 x FME: N-FORMYLMETHIONINE(Non-covalent)

FME.7: 13 residues within 4Å: Chain A: G.44, V.45, G.46, Q.51, Y.69, E.97, G.98, F.134, H.141, E.142, H.145 Ligands: CD.2, ALA.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.45 Hydrogen bonds: A:V.45, A:G.46, A:G.46, A:Q.51 FME.16: 13 residues within 4Å: Chain B: G.44, V.45, G.46, Q.51, Y.69, E.97, G.98, F.134, H.141, E.142, H.145 Ligands: CD.11, ALA.17 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.45 Hydrogen bonds: B:V.45, B:G.46, B:G.46, B:Q.51

2 x ALA: ALANINE(Non-covalent)

ALA.8: 5 residues within 4Å: Chain A: R.68, Y.69, G.98, L.100 Ligands: FME.7 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:L.100 Hydrogen bonds: A:G.98, A:G.98, A:G.98, A.8 Water bridges: A:L.100 Salt bridges: A:R.68 ALA.17: 5 residues within 4Å: Chain B: R.68, Y.69, G.98, L.100 Ligands: FME.16 8 PLIP interactions: 7 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:L.100 Hydrogen bonds: B:Y.69, B:G.98, B:G.98, B:G.98, A.17 Water bridges: B:L.100 Salt bridges: B:R.68

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 2 residues within 4Å: Chain A: N.22, E.27 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.22 GOL.18: 2 residues within 4Å: Chain B: N.22, E.27 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ngo, H.P.T. et al., Substrate complex structure of Xoo1075, a peptide deformylase, from Xanthomonas oryzae pv. oryzae. To be Published

Release Date

2014-12-03

Peptides

Peptide deformylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Peptide deformylase

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