SMTL ID : 1y6h.2 (1 other biounit)

Crystal structure of LIPDF

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: Q.53, C.101, H.143, H.147 Ligands: FMT.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.101, A:H.143, A:H.147 ZN.5: 5 residues within 4Å: Chain B: Q.53, C.101, H.143, H.147 Ligands: FMT.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.101, B:H.143, B:H.147 ZN.12: 5 residues within 4Å: Chain C: Q.53, C.101, H.143, H.147 Ligands: FMT.15 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.101, C:H.143, C:H.147 ZN.16: 5 residues within 4Å: Chain D: Q.53, C.101, H.143, H.147 Ligands: FMT.18 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.101, D:H.143, D:H.147

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

FMT.2: 5 residues within 4Å: Chain A: R.80, W.121, I.133, K.137, Y.141 Ligand excluded by PLIP FMT.3: 6 residues within 4Å: Chain A: G.106, F.165, N.166, E.167, T.168 Chain B: R.7 Ligand excluded by PLIP FMT.4: 9 residues within 4Å: Chain A: G.48, L.49, Q.53, C.101, L.102, H.143, E.144, H.147 Ligands: ZN.1 Ligand excluded by PLIP FMT.7: 9 residues within 4Å: Chain B: G.48, Q.53, C.101, L.102, H.143, E.144, H.147 Ligands: ZN.5, FMT.8 Ligand excluded by PLIP FMT.8: 10 residues within 4Å: Chain B: G.46, V.47, G.48, R.70, Y.71, G.100, C.101, L.102 Ligands: GLY.6, FMT.7 Ligand excluded by PLIP FMT.9: 5 residues within 4Å: Chain B: N.84, V.86, Q.120, W.121, Q.128 Ligand excluded by PLIP FMT.10: 1 residues within 4Å: Chain B: H.173 Ligand excluded by PLIP FMT.11: 5 residues within 4Å: Chain A: P.11, K.15 Chain B: H.173, N.174, V.175 Ligand excluded by PLIP FMT.13: 5 residues within 4Å: Chain C: R.80, W.121, I.133, K.137, Y.141 Ligand excluded by PLIP FMT.14: 6 residues within 4Å: Chain C: G.106, F.165, N.166, E.167, T.168 Chain D: R.7 Ligand excluded by PLIP FMT.15: 9 residues within 4Å: Chain C: G.48, L.49, Q.53, C.101, L.102, H.143, E.144, H.147 Ligands: ZN.12 Ligand excluded by PLIP FMT.18: 9 residues within 4Å: Chain D: G.48, Q.53, C.101, L.102, H.143, E.144, H.147 Ligands: ZN.16, FMT.19 Ligand excluded by PLIP FMT.19: 10 residues within 4Å: Chain D: G.46, V.47, G.48, R.70, Y.71, G.100, C.101, L.102 Ligands: GLY.17, FMT.18 Ligand excluded by PLIP FMT.20: 5 residues within 4Å: Chain D: N.84, V.86, Q.120, W.121, Q.128 Ligand excluded by PLIP FMT.21: 1 residues within 4Å: Chain D: H.173 Ligand excluded by PLIP FMT.22: 5 residues within 4Å: Chain C: P.11, K.15 Chain D: H.173, N.174, V.175 Ligand excluded by PLIP

2 x GLY: GLYCINE(Non-covalent)

GLY.6: 10 residues within 4Å: Chain B: V.47, Y.71, F.97, E.99, G.100, Y.136, V.140, H.143, E.144 Ligands: FMT.8 7 PLIP interactions: 6 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:E.99, B:E.99, B:G.100, B:E.144, B:E.144, G.6 Salt bridges: B:H.143 GLY.17: 10 residues within 4Å: Chain D: V.47, Y.71, F.97, E.99, G.100, Y.136, V.140, H.143, E.144 Ligands: FMT.19 6 PLIP interactions: 1 Ligand-Ligand interactions, 5 interactions with chain D Hydrogen bonds: G.17, D:E.99, D:G.100, D:Y.136, D:E.144 Salt bridges: D:H.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, Z. et al., Unique structural characteristics of peptide deformylase from pathogenic bacterium Leptospira interrogans. J.Mol.Biol. (2004)

Release Date

2004-12-21

Peptides

Peptide deformylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Peptide deformylase

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