SMTL ID : 5cwx.1

Structure of Xoo1075, a peptide deformylase from Xanthomonas oryzae pv oryzae, in complex with fragment 134

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

6 x CD: CADMIUM ION(Non-covalent)

CD.1: 4 residues within 4Å: Chain A: Q.51, C.99, H.141, H.145 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.99, A:H.141, A:H.145 CD.2: 2 residues within 4Å: Chain A: E.128, E.130 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.128, A:E.128, A:E.130, A:E.130 CD.3: 2 residues within 4Å: Chain A: M.1, E.37 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.37, H2O.3 CD.6: 4 residues within 4Å: Chain B: Q.51, C.99, H.141, H.145 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.99, B:H.141, B:H.145 CD.7: 2 residues within 4Å: Chain B: E.128, E.130 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.128, B:E.128, B:E.130, B:E.130 CD.8: 2 residues within 4Å: Chain B: M.1, E.37 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.37, H2O.6

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 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.9: 7 residues within 4Å: Chain A: F.158, D.159 Chain B: L.14, G.148, R.149, L.150, S.153 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.14 Hydrogen bonds: B:L.150, B:S.153 Water bridges: B:S.153 Salt bridges: B:R.149

2 x 56K: 3-(2-methyl-1,3-thiazol-4-yl)aniline(Non-covalent)

56K.5: 8 residues within 4Å: Chain A: V.45, W.96, E.97, G.98, F.134, R.137, H.141, E.142 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.45, A:E.97, A:F.134, A:R.137, A:H.141 Hydrogen bonds: A:E.142 Water bridges: A:V.45, A:L.100 56K.10: 8 residues within 4Å: Chain B: V.45, W.96, E.97, G.98, F.134, R.137, H.141, E.142 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.45, B:E.97, B:F.134, B:R.137, B:H.141 Hydrogen bonds: B:E.142, B:E.142 Water bridges: B:V.45, B:L.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ngo, H.P.T. et al., Structure of Xoo1075, a peptide deformylase from Xanthomonas oryzae pv oryzae, in complex with fragment 134. To Be Published

Release Date

2016-08-03

Peptides

Peptide deformylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Peptide deformylase

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