SMTL ID : 1vez.1 (1 other biounit)

Crystal Structure of Peptide Deformylase from Leptospira Interrogans(LiPDF) at pH8.0

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: Q.53, C.101, H.143, H.147 Ligands: FMT.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.101, A:H.143, A:H.147 ZN.10: 5 residues within 4Å: Chain B: Q.53, C.101, H.143, H.147 Ligands: FMT.17 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.101, B:H.143, B:H.147

6 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 9 residues within 4Å: Chain A: R.70, C.101, L.102, V.104, P.105, G.106, M.107, R.108, N.166 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.70, A:C.101, A:C.101, A:V.104, A:G.106, A:M.107, A:R.108, A:R.108, A:N.166 TRS.3: 2 residues within 4Å: Chain A: R.118, Q.120 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.118, A:R.118 TRS.4: 5 residues within 4Å: Chain A: N.84, V.86, Q.120, W.121, Q.128 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.84, A:W.121 Water bridges: A:N.84, A:F.129 TRS.11: 9 residues within 4Å: Chain B: R.70, C.101, L.102, V.104, P.105, G.106, M.107, R.108, N.166 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.70, B:C.101, B:C.101, B:V.104, B:G.106, B:M.107, B:R.108, B:R.108, B:N.166 TRS.12: 2 residues within 4Å: Chain B: R.118, Q.120 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.118, B:R.118 TRS.13: 5 residues within 4Å: Chain B: N.84, V.86, Q.120, W.121, Q.128 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.84, B:W.121 Water bridges: B:N.84, B:F.129

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

FMT.5: 1 residues within 4Å: Chain A: W.98 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.108 FMT.6: 2 residues within 4Å: Chain A: W.98, Y.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.98 FMT.7: 3 residues within 4Å: Chain A: S.95, G.135, Y.136 No protein-ligand interaction detected (PLIP) FMT.8: 10 residues within 4Å: Chain A: G.48, L.49, Q.53, C.101, L.102, H.143, E.144, H.147 Ligands: ZN.1, FMT.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.53, A:L.102, A:E.144 FMT.9: 9 residues within 4Å: Chain A: G.46, V.47, G.48, R.70, Y.71, G.100, C.101, L.102 Ligands: FMT.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.47, A:G.48, A:R.70, A:R.70, A:G.100, A:L.102 FMT.14: 1 residues within 4Å: Chain B: W.98 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.108 FMT.15: 2 residues within 4Å: Chain B: W.98, Y.110 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.98 FMT.16: 3 residues within 4Å: Chain B: S.95, G.135, Y.136 No protein-ligand interaction detected (PLIP) FMT.17: 10 residues within 4Å: Chain B: G.48, L.49, Q.53, C.101, L.102, H.143, E.144, H.147 Ligands: ZN.10, FMT.18 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.53, B:L.102, B:E.144 FMT.18: 9 residues within 4Å: Chain B: G.46, V.47, G.48, R.70, Y.71, G.100, C.101, L.102 Ligands: FMT.17 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:V.47, B:G.48, B:R.70, B:R.70, B:Y.71, B:G.100, B:L.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, Z. et al., Novel conformational states of peptide deformylase from pathogenic bacterium Leptospira interrogans: implications for population shift. J.Biol.Chem. (2005)

Release Date

2005-08-23

Peptides

Peptide deformylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Peptide deformylase

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