SMTL ID : 5kob.1 (1 other biounit)

Crystal structure of a peptide deformylase from Burkholderia xenovorans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x FE2: FE (II) ION(Non-covalent)

FE2.1: 4 residues within 4Å: Chain A: Q.59, C.107, H.149, H.153 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.107, A:H.149, A:H.153, H2O.1 FE2.8: 4 residues within 4Å: Chain B: Q.59, C.107, H.149, H.153 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.107, B:H.149, B:H.153, H2O.9

15 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 5 residues within 4Å: Chain A: Y.77, E.105, G.106, V.146, H.149 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.77, A:G.106 FMT.3: 8 residues within 4Å: Chain A: G.52, A.53, G.54, R.76, Y.77, G.106, C.107, L.108 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.53, A:G.54, A:R.76, A:R.76, A:G.106, A:L.108 FMT.4: 5 residues within 4Å: Chain A: I.93, Q.148, C.151, D.152, I.155 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.152 FMT.5: 3 residues within 4Å: Chain A: W.104, L.175, F.176 No protein-ligand interaction detected (PLIP) FMT.6: 3 residues within 4Å: Chain A: P.27, Q.65, N.90 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.65 FMT.7: 2 residues within 4Å: Chain A: R.11, E.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.12, A:E.12 FMT.9: 8 residues within 4Å: Chain B: G.52, A.53, G.54, R.76, Y.77, G.106, C.107 Ligands: FMT.10 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:A.53, B:G.54, B:R.76, B:R.76, B:Y.77, B:G.106 Water bridges: B:L.108, B:L.108 FMT.10: 6 residues within 4Å: Chain B: Y.77, E.105, G.106, V.146, H.149 Ligands: FMT.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.106 FMT.11: 6 residues within 4Å: Chain B: R.76, C.107, P.111, G.112, R.114 Ligands: FMT.14 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.76, B:C.107, B:G.112, B:R.114, B:R.114 Water bridges: B:T.172 FMT.12: 4 residues within 4Å: Chain B: H.37, V.40, K.41, Q.130 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.37, B:K.41, B:Q.130 FMT.13: 2 residues within 4Å: Chain B: H.30, F.31 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.31 FMT.14: 3 residues within 4Å: Chain B: L.108, P.111 Ligands: FMT.11 No protein-ligand interaction detected (PLIP) FMT.15: 3 residues within 4Å: Chain B: F.71, G.72, H.73 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.72, B:H.73 FMT.16: 3 residues within 4Å: Chain B: F.31, N.90, F.128 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.90 FMT.17: 2 residues within 4Å: Chain B: Q.98, D.99 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mayclin, S.J. et al., Crystal structure of a peptide deformylase from Burkholderia xenovorans. to be published

Release Date

2016-07-13

Peptides

Peptide deformylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Peptide deformylase

Related Entries With Identical Sequence