SMTL ID : 6ey4.1

Periplasmic domain (residues 36-513) of GldM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 4 residues within 4Å: Chain A: K.232, A.234, F.236, E.239 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.232, A:F.236, A:E.239 EDO.2: 4 residues within 4Å: Chain A: P.256, S.258, F.259, I.265 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.259 Water bridges: A:I.265 EDO.3: 5 residues within 4Å: Chain A: R.326, G.394, I.395, Y.488, L.490 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.395 Water bridges: A:R.326 EDO.4: 2 residues within 4Å: Chain A: D.386 Ligands: EDO.5 No protein-ligand interaction detected (PLIP) EDO.5: 4 residues within 4Å: Chain A: K.387, K.388, T.389 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.389 EDO.6: 5 residues within 4Å: Chain A: K.442, G.445, Q.446, P.447 Chain B: G.470 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:K.469 Hydrogen bonds: A:K.442, A:G.445 EDO.7: 4 residues within 4Å: Chain B: K.232, A.234, F.236, E.239 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.232, B:F.236, B:E.239 EDO.8: 4 residues within 4Å: Chain B: P.256, S.258, F.259, I.265 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.259 Water bridges: B:I.265 EDO.9: 5 residues within 4Å: Chain B: R.326, G.394, I.395, Y.488, L.490 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.395 Water bridges: B:R.326 EDO.10: 2 residues within 4Å: Chain B: D.386 Ligands: EDO.11 No protein-ligand interaction detected (PLIP) EDO.11: 4 residues within 4Å: Chain B: K.387, K.388, T.389 Ligands: EDO.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.389 EDO.12: 5 residues within 4Å: Chain A: G.470 Chain B: K.442, G.445, Q.446, P.447 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.442, B:G.445 Water bridges: A:K.469

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leone, P. et al., Type IX secretion system PorM and gliding machinery GldM form arches spanning the periplasmic space. Nat Commun (2018)

Release Date

2018-02-07

Peptides

GldM: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GldM