SMTL ID : 3zeb.1

A complex of GlpG with isocoumarin inhibitor covalently bonded to serine 201 and histidine 150

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x SV1: 2-phenylethyl 2-(4-azanyl-2-methanoyl-phenyl)ethanoate(Covalent)

SV1.1: 11 residues within 4Å: Chain A: M.58, H.59, F.62, N.63, S.110, Y.114, W.145, G.149, F.154, M.156, M.158 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:H.59, A:F.62, A:F.62, A:F.154, A:F.154 Hydrogen bonds: A:N.63, A:W.145, A:G.149 Water bridges: A:S.110 Salt bridges: A:H.59 pi-Stacking: A:W.145, A:W.145

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

CL.2: 4 residues within 4Å: Chain A: H.54, F.55, S.56, H.59 Ligand excluded by PLIP

5 x BNG: nonyl beta-D-glucopyranoside(Non-covalent)

BNG.3: 6 residues within 4Å: Chain A: V.5, V.8, M.9, A.12, I.84, T.87 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.5, A:V.8, A:A.12, A:I.84, A:T.87 BNG.4: 1 residues within 4Å: Chain A: V.176 No protein-ligand interaction detected (PLIP) BNG.5: 3 residues within 4Å: Chain A: M.9, F.48, T.87 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.48, A:T.87 BNG.6: 3 residues within 4Å: Chain A: W.31, L.40, R.46 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.31, A:R.46 BNG.7: 3 residues within 4Å: Chain A: L.65, W.66, L.138 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.65, A:L.65, A:W.66, A:W.66, A:L.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vosyka, O. et al., Activity-Based Probes for Rhomboid Proteases Discovered in a Mass Spectrometry-Based Assay. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-02-13

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

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