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

Crystal structure of GlpG, a rhomboid intramembrane serine protease

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 5 residues within 4Å: Chain A: W.121, R.136, G.137, I.139 Ligands: LDA.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.137

13 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)(Non-functional Binders)

LDA.2: 5 residues within 4Å: Chain A: V.15, I.18, I.22, L.23 Ligands: LDA.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.15, A:I.18, A:I.18, A:I.22, A:L.23 LDA.3: 4 residues within 4Å: Chain A: W.7, I.11 Ligands: LDA.2, LDA.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.7, A:W.7, A:I.11 LDA.4: 6 residues within 4Å: Chain A: G.3, P.4, V.8, I.11 Ligands: LDA.3, LDA.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.4, A:V.8, A:I.11 Hydrogen bonds: A:G.3 LDA.5: 8 residues within 4Å: Chain A: M.10, V.14, F.17, L.57, L.61, L.64, L.65, W.68 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.14, A:V.14, A:F.17, A:L.57, A:L.61, A:L.64 LDA.6: 3 residues within 4Å: Chain A: V.5, S.80 Ligands: LDA.7 No protein-ligand interaction detected (PLIP) LDA.7: 3 residues within 4Å: Chain A: P.4 Ligands: LDA.4, LDA.6 No protein-ligand interaction detected (PLIP) LDA.8: 3 residues within 4Å: Chain A: W.150 Ligands: LDA.12, LMT.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.150, A:W.150, A:W.150 LDA.9: 3 residues within 4Å: Chain A: W.150, F.151 Ligands: LDA.14 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.151, A:F.151, A:F.151 Water bridges: A:F.151 LDA.10: 1 residues within 4Å: Ligands: LDA.11 No protein-ligand interaction detected (PLIP) LDA.11: 2 residues within 4Å: Chain A: W.45 Ligands: LDA.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.45 LDA.12: 2 residues within 4Å: Ligands: LDA.8, LDA.14 No protein-ligand interaction detected (PLIP) LDA.13: 5 residues within 4Å: Chain A: W.121, I.139, I.140, L.143 Ligands: PO4.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.121, A:L.143, A:L.143 LDA.14: 2 residues within 4Å: Ligands: LDA.9, LDA.12 No protein-ligand interaction detected (PLIP)

1 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.15: 9 residues within 4Å: Chain A: L.93, F.101, S.102, S.157, M.158, G.161, A.165, A.168 Ligands: LDA.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.93, A:A.165, A:A.168 Hydrogen bonds: A:S.102, A:S.157, A:S.157, A:M.158, A:G.161 Water bridges: A:W.150

4 x PGV: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(Non-covalent)(Non-functional Binders)

PGV.16: 9 residues within 4Å: Chain A: H.59, F.62, N.63, W.66, S.110, Y.114, F.141, W.145, H.163 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.62, A:F.62, A:F.141 Hydrogen bonds: A:N.63, A:N.63, A:S.110 Water bridges: A:N.63, A:S.110 Salt bridges: A:H.59, A:H.163, A:H.163 PGV.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PGV.18: 3 residues within 4Å: Chain A: W.66, L.138, F.141 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.66, A:F.141 PGV.19: 3 residues within 4Å: Chain A: W.145, F.154, M.156 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.145, A:F.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ben-Shem, A. et al., Structural basis for intramembrane proteolysis by rhomboid serine proteases. Proc.Natl.Acad.Sci.Usa (2007)

Release Date

2006-10-31

Peptides

Protein glpG: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Membrane

We predict this structure to be a membrane protein.
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Protein glpG

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