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

Crystal structure of 3'SL bound ArtB

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-pentamer

Ligands

3 x GLC- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose

GLC-GAL-SIA.1: 8 residues within 4Å: Chain C: S.45, G.46, I.72, F.75, V.107, W.108, T.109, D.110 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:T.109, C:S.45, C:G.46, C:T.109, C:D.110 Hydrophobic interactions: C:I.72 Water bridges: C:S.45, C:G.46, C:G.76, C:G.76 Salt bridges: C:K.48 GLC-GAL-SIA.3: 9 residues within 4Å: Chain D: S.45, G.46, I.72, F.75, G.76, V.107, W.108, T.109, D.110 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.72 Hydrogen bonds: D:S.45, D:G.46, D:G.76, D:T.109, D:D.110 Water bridges: D:S.45, D:D.110 GLC-GAL-SIA.4: 9 residues within 4Å: Chain E: S.45, G.46, I.72, F.75, G.76, V.107, W.108, T.109, D.110 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:I.72, E:F.75 Hydrogen bonds: E:S.45, E:G.76, E:T.109, E:D.110 Salt bridges: E:K.48

1 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose(Non-covalent)

GAL-SIA.2: 9 residues within 4Å: Chain D: T.28, Y.29, Q.30, S.31, N.32, R.59, P.64, N.65, Y.103 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:N.32, D:Y.29, D:Y.29, D:S.31, D:R.59, D:R.59, D:N.65, D:N.65 Hydrophobic interactions: D:T.28 Water bridges: D:Y.29

6 x CA: CALCIUM ION(Non-covalent)

CA.5: 2 residues within 4Å: Chain A: C.128 Chain D: Y.93 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:C.128, H2O.1, H2O.2, H2O.7 CA.13: 1 residues within 4Å: Chain B: C.128 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:C.128, H2O.2, H2O.4, H2O.5 CA.19: 1 residues within 4Å: Chain C: D.132 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.132, C:D.132, H2O.5, H2O.6 CA.20: 1 residues within 4Å: Chain C: C.128 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:C.128, H2O.1, H2O.4, H2O.6 CA.27: 2 residues within 4Å: Chain D: C.128 Chain E: Y.93 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:C.128, H2O.6, H2O.7, H2O.9 CA.33: 1 residues within 4Å: Chain E: C.128 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:C.128, H2O.4, H2O.4, H2O.8

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

PEG.6: 3 residues within 4Å: Chain A: N.36, V.63 Chain C: T.129 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.36 PEG.7: 8 residues within 4Å: Chain A: D.73, K.79, Q.80, G.81, F.82, D.83, N.84 Chain D: Q.51 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:K.79, A:F.82, A:D.83, A:N.84, D:Q.51 Water bridges: A:G.81, A:N.84, D:Q.51 PEG.8: 7 residues within 4Å: Chain A: R.90, Y.91, A.94 Chain C: Y.91 Chain D: A.94 Ligands: PEG.21, CL.31 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.90 PEG.14: 7 residues within 4Å: Chain B: S.45, F.75, V.107, W.108, T.109, D.110 Ligands: CL.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.45, B:T.109 PEG.15: 5 residues within 4Å: Chain B: A.87, R.90, Y.91, A.94 Chain E: Y.91 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.90 PEG.21: 6 residues within 4Å: Chain B: Y.91 Chain C: A.87, R.90, Y.91, A.94 Ligands: PEG.8 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.87, C:R.90 PEG.22: 3 residues within 4Å: Chain C: P.140, N.141, H.144 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.141 PEG.23: 8 residues within 4Å: Chain B: N.22, M.23, P.137, T.138 Chain C: R.111, N.112, A.115, A.116 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:N.112, C:A.116, B:N.22, B:T.138 PEG.34: 2 residues within 4Å: Chain E: E.143, H.144 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:H.144

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

CL.9: 3 residues within 4Å: Chain A: V.66, H.67, T.68 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: Q.30, P.64, N.65, V.66 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: N.27, Y.29 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain B: V.66, H.67, T.68 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain B: F.75, T.109 Ligands: PEG.14 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain C: V.66, H.67, T.68, N.120 Ligand excluded by PLIP CL.25: 1 residues within 4Å: Chain C: A.94 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain D: Y.43, D.110, N.112 Ligand excluded by PLIP CL.29: 4 residues within 4Å: Chain D: V.66, H.67, T.68, N.120 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain D: E.97, D.98 Ligand excluded by PLIP CL.31: 1 residues within 4Å: Ligands: PEG.8 Ligand excluded by PLIP CL.35: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.36: 4 residues within 4Å: Chain E: V.66, H.67, T.68, N.120 Ligand excluded by PLIP

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

MES.12: 5 residues within 4Å: Chain B: N.27, T.28, Y.29, S.31, R.59 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.29, B:S.31, B:R.59 pi-Cation interactions: B:Y.29 MES.18: 6 residues within 4Å: Chain C: N.27, T.28, Y.29, Q.30, S.31, R.59 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.29, C:S.31 Salt bridges: C:R.59 MES.32: 7 residues within 4Å: Chain E: N.27, T.28, Y.29, Q.30, S.31, R.59, D.132 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Y.29, E:S.31, E:D.132

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.26: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.83

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

Related Entries With Identical Sequence