SMTL ID : 4e9b.1

Structure of Peptide Deformylase form Helicobacter Pylori in complex with actinonin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x CO: COBALT (II) ION(Non-covalent)

CO.1: 5 residues within 4Å: Chain A: Q.50, C.95, H.137, H.141 Ligands: BB2.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.95, A:H.137, A:H.141

1 x BB2: ACTINONIN(Non-covalent)

BB2.2: 16 residues within 4Å: Chain A: G.43, I.44, G.45, Q.50, Y.91, K.92, E.93, G.94, C.95, L.96, Y.102, V.133, H.137, E.138, H.141 Ligands: CO.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.44, A:E.93, A:L.96, A:Y.102, A:V.133, A:H.137 Hydrogen bonds: A:I.44, A:G.45, A:Q.50, A:G.94, A:G.94, A:L.96, A:E.138

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.3: 4 residues within 4Å: Chain A: E.19, R.56, N.143 Ligands: DMS.5 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.19

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 4 residues within 4Å: Chain A: I.60, N.61, L.62, D.73 No protein-ligand interaction detected (PLIP) DMS.5: 5 residues within 4Å: Chain A: I.16, S.17, K.18, E.19 Ligands: EPE.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.18 Salt bridges: A:E.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cui, K. et al., Identification of Novel Peptide Deformylase Inhibitors from Natural Products. To be Published

Release Date

2013-04-24

Peptides

Peptide deformylase 11: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peptide deformylase 11

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