SMTL ID : 5whv.1 (1 other biounit)

Crystal structure of ArtB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-pentamer

Ligands

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

PEG.1: 5 residues within 4Å: Chain A: Y.93, A.94 Chain C: Y.91, T.95, E.97 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Water bridges: C:Y.91, C:Y.91 Hydrogen bonds: A:Y.93 PEG.5: 10 residues within 4Å: Chain B: Y.43, S.45, I.72, F.75, G.76, V.107, W.108, T.109, D.110, F.113 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.45, B:S.45, B:T.109, B:D.110 PEG.6: 7 residues within 4Å: Chain B: N.112, A.115, A.116 Chain E: G.136, P.137, T.138 Ligands: CL.18 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:G.136, E:T.138, B:N.112 Water bridges: E:T.138 PEG.10: 9 residues within 4Å: Chain C: S.45, I.72, F.75, G.76, V.107, W.108, T.109, D.110, F.113 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.45, C:T.109 Water bridges: C:G.76, C:G.76 PEG.13: 9 residues within 4Å: Chain D: Y.43, S.45, I.72, F.75, V.107, W.108, T.109, D.110, F.113 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.45, D:S.45, D:T.109 PEG.15: 8 residues within 4Å: Chain E: S.45, F.75, G.76, K.79, V.107, W.108, T.109, D.110 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:G.76, E:G.76, E:T.109, E:D.110 Water bridges: E:S.45, E:S.45 PEG.16: 6 residues within 4Å: Chain E: Q.34, K.58, T.95, G.96, E.97, D.98 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:D.98 Water bridges: E:K.58, E:K.58, E:K.58, E:D.98 PEG.17: 5 residues within 4Å: Chain E: N.27, T.28, Y.29, Q.30, L.139 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.29

3 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 7 residues within 4Å: Chain A: N.27, T.28, Y.29, Q.30, S.31, R.59, Y.103 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.29, A:S.31 Salt bridges: A:R.59 MES.7: 9 residues within 4Å: Chain B: N.27, T.28, Y.29, Q.30, S.31, R.59, N.65, Y.103, L.139 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.29, B:S.31 Salt bridges: B:R.59 MES.11: 6 residues within 4Å: Chain C: N.27, T.28, Y.29, Q.30, S.31, R.59 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.29, C:Y.29, C:S.31 Salt bridges: C:R.59

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

CL.3: 4 residues within 4Å: Chain A: V.66, H.67, T.68, N.120 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: V.66, H.67, T.68, N.120 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain C: V.66, H.67, T.68, N.120 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain D: V.66, H.67, T.68, N.120 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain E: N.22, M.23, P.137 Ligands: PEG.6 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain E: V.66, H.67, T.68, N.120 Ligand excluded by PLIP

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 1 residues within 4Å: Chain A: C.128 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:C.128, H2O.1, H2O.1, H2O.7 CA.9: 1 residues within 4Å: Chain B: C.128 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.128, H2O.3, H2O.4 CA.20: 2 residues within 4Å: Chain B: Y.93 Chain E: C.128 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:C.128, H2O.3, H2O.4, H2O.9, H2O.11 CA.21: 1 residues within 4Å: Chain E: T.95 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:T.95, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, X. et al., Evolution of host adaptation in the Salmonella typhoid toxin. Nat Microbiol (2017)

Release Date

2017-10-25

Peptides

ArtB protein: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

ArtB protein

Related Entries With Identical Sequence