SMTL ID : 5whu.1 (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

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

GAL-SIA.1: 7 residues within 4Å: Chain A: T.28, Y.29, Q.30, S.31, N.32, R.59, N.65 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.28 Hydrogen bonds: A:Y.29, A:Y.29, A:S.31, A:R.59, A:R.59, A:N.65 Water bridges: A:Y.29 Salt bridges: A:R.59 GAL-SIA.4: 8 residues within 4Å: Chain E: Y.29, Q.30, S.31, N.32, R.59, P.64, N.65, Y.103 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:N.32, E:Y.29, E:S.31, E:R.59, E:R.59, E:N.65, E:N.65 Water bridges: E:Y.29

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

GLC-GAL-SIA.2: 9 residues within 4Å: Chain C: S.45, G.46, I.72, F.75, G.76, V.107, W.108, T.109, D.110 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.72, C:F.75, C:D.110 Hydrogen bonds: C:S.45, C:G.76, C:T.109, C:D.110 Water bridges: C:G.46, C:K.48, C:K.79 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 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:T.109, D:S.45, D:G.76, D:T.109, D:D.110 Hydrophobic interactions: D:I.72, D:W.108, D:D.110 Water bridges: D:S.45, D:G.46 GLC-GAL-SIA.5: 9 residues within 4Å: Chain E: S.45, G.46, I.72, F.75, G.76, V.107, W.108, T.109, D.110 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:T.109, E:S.45, E:G.76, E:T.109, E:D.110 Hydrophobic interactions: E:I.72

1 x SIA: N-acetyl-alpha-neuraminic acid(Non-functional Binders)

SIA.6: 9 residues within 4Å: Chain A: S.45, G.46, I.72, F.75, G.76, V.107, W.108, T.109, D.110 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.72, A:F.75 Hydrogen bonds: A:S.45, A:G.76, A:T.109, A:D.110

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

PEG.7: 1 residues within 4Å: Chain A: D.98 No protein-ligand interaction detected (PLIP) PEG.13: 7 residues within 4Å: Chain B: I.72, F.75, G.76, V.107, W.108, T.109, D.110 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.76, B:T.109 PEG.23: 5 residues within 4Å: Chain E: Q.34, T.95, G.96, E.97, D.98 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.95 Water bridges: E:D.98, E:D.98

10 x CL: CHLORIDE ION(Non-functional Binders)(Non-covalent)

CL.8: 2 residues within 4Å: Chain A: R.90, Y.91 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: D.25, Y.26, N.27, T.28 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: H.67, T.68, N.120 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain D: N.112 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: H.67, T.68, N.120 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain B: C.128 Ligand excluded by PLIP CL.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain C: V.66, H.67, T.68, N.120 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain D: V.66, H.67, T.68, N.120 Ligand excluded by PLIP CL.24: 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-functional Binders)(Non-covalent)

MES.12: 6 residues within 4Å: Chain B: N.27, T.28, Y.29, Q.30, S.31, R.59 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.17: 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.19: 5 residues within 4Å: Chain D: N.27, Y.29, Q.30, S.31, R.59 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.29, D:S.31, D:S.31 Salt bridges: D:R.59

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

TRS.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.22: 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.3, H2O.8, H2O.9

Links

RCSB   PDBe   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

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