SMTL ID : 5cx0.1

Structure of Xoo1075, a peptide deformylase from Xanthomonas oryzae pv. oryzae, in complex with fragment 322

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

6 x CD: CADMIUM ION(Non-covalent)

CD.1: 5 residues within 4Å: Chain A: Q.51, C.99, H.141, H.145 Ligands: 56L.5 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: M.1, E.37 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.37, H2O.3, 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.130, A:E.130, H2O.1, H2O.2 CD.6: 5 residues within 4Å: Chain B: Q.51, C.99, H.141, H.145 Ligands: 56L.10 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: M.1, E.37 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.37, H2O.5, H2O.5 CD.8: 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.130, B:E.130, H2O.4, H2O.5

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 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.158 Hydrogen bonds: B:D.159, A:L.150, A:S.153 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: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.158 Hydrogen bonds: A:D.159, A:D.159, B:L.150, B:S.153

2 x 56L: 5-(propan-2-yl)-2-thioxodihydropyrimidine-4,6(1H,5H)-dione(Non-covalent)

56L.5: 12 residues within 4Å: Chain A: V.45, G.46, Q.51, E.97, G.98, C.99, L.100, R.137, V.138, H.141, E.142 Ligands: CD.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.45, A:E.97, A:R.137 Hydrogen bonds: A:G.46, A:G.98, A:G.98 Water bridges: A:V.45, A:G.46 56L.10: 12 residues within 4Å: Chain B: V.45, G.46, Q.51, E.97, G.98, C.99, L.100, R.137, V.138, H.141, E.142 Ligands: CD.6 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.45, B:E.97, B:R.137 Hydrogen bonds: B:G.46, B:G.98, B:G.98, B:E.142 Water bridges: B:V.45, B:G.46

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 322. 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

Related Entries With Identical Sequence