SMTL ID : 5whv.2 (1 other biounit)

Crystal structure of ArtB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-pentamer

Ligands

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

PEG.1: 4 residues within 4Å: Chain A: T.28, V.66, E.105 Ligands: PEG.3 No protein-ligand interaction detected (PLIP) PEG.2: 7 residues within 4Å: Chain A: N.36, K.58, S.61, Q.62, V.63 Chain C: T.129, Y.133 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.36 Water bridges: A:N.37 PEG.3: 6 residues within 4Å: Chain A: N.27, T.28, Y.29, Y.103, L.139 Ligands: PEG.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.31, A:E.105 PEG.4: 7 residues within 4Å: Chain A: F.75, G.76, K.79, V.107, W.108, T.109, D.110 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.76, A:K.79, A:K.79, A:T.109, A:D.110 Water bridges: A:D.110 PEG.5: 3 residues within 4Å: Chain A: D.83, N.84 Chain D: D.83 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.84 Water bridges: A:D.83 PEG.8: 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 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.45, B:G.76, B:T.109, B:D.110 Water bridges: B:G.76 PEG.9: 7 residues within 4Å: Chain B: N.22, M.23, P.137, T.138 Chain C: N.112, A.115, A.116 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.23, B:T.138 PEG.13: 9 residues within 4Å: Chain C: S.45, I.72, F.75, V.107, W.108, T.109, D.110, F.113 Ligands: PEG.15 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.45, C:S.45, C:T.109, C:D.110 PEG.14: 7 residues within 4Å: Chain C: N.65, V.66, H.67, T.68, S.118, G.119, N.120 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:H.67, C:H.67, C:T.68, C:T.68, C:G.119, C:N.120 PEG.15: 8 residues within 4Å: Chain C: S.45, G.46, D.47, K.48, F.75, T.109, D.110 Ligands: PEG.13 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.47, C:T.109 PEG.18: 9 residues within 4Å: Chain D: Y.43, S.45, I.72, F.75, V.107, W.108, T.109, D.110, F.113 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.45, D:V.107, D:D.110, D:D.110 PEG.19: 1 residues within 4Å: Chain D: R.111 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.111 PEG.24: 9 residues within 4Å: Chain E: Y.43, S.45, I.72, F.75, V.107, W.108, T.109, D.110, F.113 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:S.45, E:S.45, E:V.107, E:T.109, E:D.110

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

CL.6: 4 residues within 4Å: Chain A: V.66, H.67, T.68, N.120 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: H.67, T.68, N.120 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain D: N.36, N.37, G.56, L.57 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain D: V.66, H.67, T.68, N.120 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain E: H.67, T.68, N.120 Ligand excluded by PLIP

5 x CA: CALCIUM ION(Non-covalent)

CA.7: 1 residues within 4Å: Chain A: C.128 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:C.128, H2O.1, H2O.3, H2O.11, H2O.11 CA.12: 2 residues within 4Å: Chain B: C.128 Chain C: Y.93 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:C.128, H2O.4, H2O.6, H2O.7 CA.17: 1 residues within 4Å: Chain C: C.128 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:C.128, H2O.6, H2O.7 CA.23: 1 residues within 4Å: Chain D: C.128 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:C.128, H2O.10, H2O.10, H2O.12, H2O.15 CA.27: 1 residues within 4Å: Chain E: C.128 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:C.128, H2O.5, H2O.13, H2O.14, H2O.16

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

MES.10: 8 residues within 4Å: Chain B: N.27, T.28, Y.29, Q.30, S.31, R.59, Y.103, L.139 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.29, B:Y.29, B:S.31 Salt bridges: B:R.59 MES.16: 8 residues within 4Å: Chain C: N.27, T.28, Y.29, Q.30, S.31, R.59, Y.103, L.139 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.29, C:S.31 Water bridges: C:S.31 Salt bridges: C:R.59 MES.20: 8 residues within 4Å: Chain D: N.27, T.28, Y.29, Q.30, S.31, R.59, Y.103, L.139 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.29, D:Y.29, D:S.31 Salt bridges: D:R.59 MES.25: 8 residues within 4Å: Chain E: N.27, T.28, Y.29, Q.30, S.31, R.59, Y.103, L.139 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Y.29, E:Y.29, E:S.31 Water bridges: E:S.31 Salt bridges: E:R.59

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
F

B
G

C
H

D
I

E
J

ArtB protein

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