SMTL ID : 1icj.1

PDF PROTEIN IS CRYSTALLIZED AS NI2+ CONTAINING FORM, COCRYSTALLIZED WITH INHIBITOR POLYETHYLENE GLYCOL (PEG)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

3 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 4 residues within 4Å: Chain A: Q.50, C.90, H.132, H.136 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.90, A:H.132, A:H.136, H2O.2 NI.3: 4 residues within 4Å: Chain B: Q.50, C.90, H.132, H.136 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.90, B:H.132, B:H.136, H2O.4 NI.7: 4 residues within 4Å: Chain C: Q.50, C.90, H.132, H.136 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.90, C:H.132, C:H.136, H2O.7

3 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.2: 15 residues within 4Å: Chain A: E.41, E.42, G.43, I.44, G.45, E.88, G.89, C.90, L.91, P.94, E.95, R.97, C.129, H.132, E.133 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:I.44, A:G.45, A:G.89, A:C.90, A:E.95 Water bridges: A:C.90, A:L.91 2PE.6: 13 residues within 4Å: Chain B: E.41, E.42, G.43, I.44, G.45, E.87, E.88, G.89, L.91, R.97, C.129, H.132, E.133 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.42, B:E.42, B:I.44, B:R.97 Water bridges: B:L.91 2PE.8: 14 residues within 4Å: Chain C: E.42, G.43, I.44, G.45, E.87, E.88, G.89, C.90, P.94, E.95, R.97, C.129, H.132, E.133 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:I.44, C:G.45, C:G.89, C:E.95, C:R.97, C:R.97 Water bridges: C:C.90, C:L.91

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain B: I.53, H.54, Q.55 Chain C: R.29 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Salt bridges: C:R.29 Hydrogen bonds: B:H.54, B:Q.55 SO4.5: 5 residues within 4Å: Chain B: R.29 Chain C: D.52, I.53, H.54, Q.55 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Salt bridges: B:R.29 Hydrogen bonds: C:D.52, C:H.54, C:Q.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Becker, A. et al., Structure of peptide deformylase and identification of the substrate binding site. J.Biol.Chem. (1998)

Release Date

1999-03-23

Peptides

PEPTIDE DEFORMYLASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

PEPTIDE DEFORMYLASE

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