SMTL ID : 5y3z.1

Structure of the periplasmic domain of the MotB L119P mutant from Salmonella (crystal form 1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

3 x ARG: ARGININE(Non-covalent)

ARG.1: 10 residues within 4Å: Chain A: T.66, G.67, T.99, D.100, F.102, Y.104, N.113, L.116, R.120, R.161 13 PLIP interactions: 10 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:F.102 Hydrogen bonds: A:T.66, A:G.67, A:D.100, A:D.100, A:F.102, A:F.102, A:N.113, R.1 Salt bridges: A:R.120, A:R.161 Water bridges: R.1, R.1 ARG.2: 7 residues within 4Å: Chain A: Q.59, N.60, R.61, P.62, D.156, A.158, R.161 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:P.62, A:A.158 Hydrogen bonds: A:Q.59, R.2, R.2 Salt bridges: A:R.161 ARG.6: 11 residues within 4Å: Chain B: T.66, G.67, T.99, D.100, F.102, P.103, Y.104, N.113, L.116, R.120, R.161 12 PLIP interactions: 1 Ligand-Ligand interactions, 11 interactions with chain B Hydrogen bonds: R.6, B:G.67, B:D.100, B:D.100, B:F.102, B:P.103, B:A.105, B:N.113 Hydrophobic interactions: B:T.66, B:Y.104 Salt bridges: B:R.120, B:R.161

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.3: 7 residues within 4Å: Chain A: S.94, L.95, A.96, R.140, S.164, L.165, L.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.94, A:R.140 IMD.7: 4 residues within 4Å: Chain B: S.94, A.96, S.164, L.166 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.94

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 6 residues within 4Å: Chain A: G.50, L.51, N.91, V.167, L.168, N.169 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.51, A:V.167 Hydrogen bonds: A:N.91 Water bridges: A:N.91 MPD.5: 3 residues within 4Å: Chain A: R.80, A.130 Chain B: K.109 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.130 MPD.8: 3 residues within 4Å: Chain B: N.91, V.167, N.169 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.167, B:N.169 Hydrogen bonds: B:N.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kojima, S. et al., The Helix Rearrangement in the Periplasmic Domain of the Flagellar Stator B Subunit Activates Peptidoglycan Binding and Ion Influx. Structure (2018)

Release Date

2018-04-11

Peptides

Motility protein B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Motility protein B

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