SMTL ID : 5jbs.1

Conformational changes during monomer-to-dimer transition of Brucella suis VirB8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: W.10, N.124, P.125, L.126 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain B: W.10, N.124, P.125, L.126, G.127 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: R.134, D.136, P.137 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.134, A:D.136, A:D.136

5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 8 residues within 4Å: Chain A: Y.9, W.10, L.122, T.123, P.125 Chain B: W.10, T.123, P.125 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.9, A:Y.9, B:T.123 Water bridges: A:Q.13 PEG.6: 7 residues within 4Å: Chain B: S.38, S.40, E.41, T.131 Chain C: N.75, K.77, I.79 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.38, B:E.41, C:N.75, C:K.77 PEG.8: 8 residues within 4Å: Chain C: Y.30, E.31, G.34, M.35, A.46 Chain D: W.102, P.137 Ligands: EPE.7 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:M.35 Water bridges: C:G.34, C:G.34 PEG.9: 7 residues within 4Å: Chain C: D.3, R.6, D.7, G.76, G.78, Y.108, Q.109 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.6 Water bridges: C:G.76, C:Y.110 PEG.11: 4 residues within 4Å: Chain D: Y.9, W.10, T.123, P.125 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.9 Water bridges: D:Q.13

3 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 6 residues within 4Å: Chain B: I.16, T.20, D.22, T.25, D.29, V.67 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.22, B:D.22 Water bridges: B:V.67 Salt bridges: B:D.29, B:D.29 EPE.7: 7 residues within 4Å: Chain C: Q.43, A.46 Chain D: E.19, K.86, W.102, V.135 Ligands: PEG.8 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.19 Salt bridges: D:E.19 EPE.10: 7 residues within 4Å: Chain C: I.16, A.17, T.20, T.25, D.29, R.64, V.67 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.25, C:V.67 Water bridges: C:D.29, C:D.29 Salt bridges: C:D.29, C:D.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arya, T. et al., NMR analyses, X-ray crystallography and small-molecule probing reveal conformational shifts during monomer-to-dimer transition of Brucella suis VirB8. To Be Published

Release Date

2017-03-01

Peptides

Type IV secretion system protein virB8: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Type IV secretion system protein virB8