SMTL ID : 3zot.1

Structure of E.coli rhomboid protease GlpG in complex with monobactam L29 (data set 2)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x L6C: phenyl N-[(1R)-3-oxidanylidene-1-phenyl-propyl]carbamate(Covalent)

L6C.1: 12 residues within 4Å: Chain A: M.58, H.59, F.62, N.63, W.66, S.110, V.113, Y.114, A.142, W.145, F.154, H.163 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.62, A:W.145, A:W.145, A:W.145, A:F.154 Hydrogen bonds: A:N.63 pi-Stacking: A:W.66, A:W.66, A:Y.114

9 x BNG: nonyl beta-D-glucopyranoside(Non-functional Binders)(Non-covalent)

BNG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) BNG.3: 1 residues within 4Å: Chain A: V.176 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.176 BNG.4: 2 residues within 4Å: Chain A: F.42, F.44 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.42, A:F.42, A:F.44 BNG.5: 3 residues within 4Å: Chain A: V.16, A.19, W.31 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.16, A:A.19, A:W.31 BNG.6: 1 residues within 4Å: Chain A: D.37 No protein-ligand interaction detected (PLIP) BNG.7: 5 residues within 4Å: Chain A: F.48, A.51, T.87, A.91 Ligands: BNG.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.48, A:A.51, A:T.87, A:A.91 BNG.8: 2 residues within 4Å: Chain A: V.8 Ligands: BNG.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.8 BNG.9: 3 residues within 4Å: Chain A: A.12, V.16, L.52 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.12, A:V.16, A:L.52 BNG.10: 4 residues within 4Å: Chain A: W.121, E.125, R.136, I.139 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.125, A:R.136 Water bridges: A:E.125 Salt bridges: A:R.136

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 3 residues within 4Å: Chain A: K.82, R.123, D.177 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: Q.135, R.136, G.137 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vinothkumar, K.R. et al., Structure of Rhomboid Protease in Complex with Beta-Lactam Inhibitors Defines the S2' Cavity. Structure (2013)

Release Date

2013-05-22

Peptides

RHOMBOID PROTEASE GLPG: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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RHOMBOID PROTEASE GLPG