SMTL ID : 7s0z.1 (1 other biounit)

Structures of TcdB in complex with R-Ras

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

hetero-1-1-mer

Ligands

1 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.1: 19 residues within 4Å: Chain A: I.101, W.102, I.103, N.139, L.265, A.266, S.269, R.273, Y.284, D.286, V.287, D.288, E.516, S.519, L.520, W.521 Chain B: N.39 Ligands: MN.13, GLC.16 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.265, A:L.520 Hydrogen bonds: A:I.101, A:I.103, A:I.103, A:N.139, A:S.269, A:Y.284, A:D.286, A:V.287, A:S.519, A:L.520, B:N.39 Water bridges: A:I.101, A:D.288, A:Q.386, B:N.39 pi-Stacking: A:W.102

4 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.2: 7 residues within 4Å: Chain A: V.369, S.370, P.371, E.373, S.390, A.391, S.394 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.373, A:S.390, A:A.391 NH4.5: 4 residues within 4Å: Chain A: N.5, R.6, E.32, H.35 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.6 Water bridges: A:N.5, A:K.7 NH4.14: 1 residues within 4Å: Chain A: D.51 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.51 NH4.15: 1 residues within 4Å: Chain A: K.506 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.506

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: N.97, N.126, N.128, N.238, I.280 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.97, A:N.97, A:N.126, A:N.238 EDO.4: 6 residues within 4Å: Chain A: Q.257, R.262, N.412, L.415, G.416, Y.454 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.257, A:R.262, A:R.262, A:N.412, A:Y.454 Water bridges: A:E.261 EDO.6: 6 residues within 4Å: Chain A: E.245, F.246, G.249, E.250, A.275, N.279 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.250, A:N.279 Water bridges: A:G.249 EDO.9: 7 residues within 4Å: Chain A: K.480, T.484, S.493, I.494, L.495, E.498 Chain B: R.56 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.56, B:R.56, A:L.495 EDO.11: 3 residues within 4Å: Chain A: N.126, V.127, S.236 5 PLIP interactions: 5 interactions with chain A Water bridges: A:N.126, A:N.126, A:V.127, A:V.127, A:N.128 EDO.17: 5 residues within 4Å: Chain A: K.74, E.77, Y.78, I.81 Ligands: ACT.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.74, A:E.77

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 6 residues within 4Å: Chain A: S.519, L.520, W.521, Q.522, F.523 Ligands: ACT.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.531 ACT.8: 7 residues within 4Å: Chain A: I.146, R.175, G.458, F.459, Q.531, Y.535 Ligands: ACT.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.146 Hydrogen bonds: A:Q.531 Salt bridges: A:R.175 ACT.10: 5 residues within 4Å: Chain A: L.362, P.363, L.364, V.507, N.508 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.362, A:V.507 Hydrogen bonds: A:N.508 ACT.18: 3 residues within 4Å: Chain A: K.74, Y.78 Ligands: EDO.17 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.74 ACT.19: 4 residues within 4Å: Chain A: A.440, N.441, E.442 Chain B: R.77 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:E.442 Hydrogen bonds: B:R.77 Salt bridges: B:R.77

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

PEG.12: 5 residues within 4Å: Chain A: N.238, N.242, F.243, E.244, E.245 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.244, A:E.245 Water bridges: A:N.242

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.13: 4 residues within 4Å: Chain A: D.286, D.288, E.516 Ligands: UDP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.288, A:E.516, H2O.1, H2O.1

1 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.16: 13 residues within 4Å: Chain A: A.266, D.270, R.273, D.286, I.384, N.385, Q.386, T.466, G.471, P.472, W.521 Chain B: N.39 Ligands: UDP.1 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.286, A:N.385, A:W.521, B:N.39 Water bridges: A:D.286 Salt bridges: A:R.273

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.20: 18 residues within 4Å: Chain A: E.462 Chain B: G.15, G.16, G.17, V.18, G.19, K.20, S.21, A.22, F.32, N.120, K.121, D.123, L.124, S.150, A.151, K.152 Ligands: MG.21 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:G.15, B:G.17, B:V.18, B:G.19, B:K.20, B:S.21, B:A.22, B:N.120, B:K.121, B:K.121, B:A.151, B:K.152 Water bridges: B:K.20, B:S.21, B:V.33, B:D.37 Salt bridges: B:K.20, B:D.123 pi-Stacking: B:F.32, B:F.32

1 x MG: MAGNESIUM ION(Non-covalent)

MG.21: 3 residues within 4Å: Chain A: E.462 Chain B: S.21 Ligands: GDP.20 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.21, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Z. et al., Structural basis for selective modification of Rho and Ras GTPases by Clostridioides difficile toxin B. Sci Adv (2021)

Release Date

2021-09-08

Peptides

Toxin B: A
Ras-related protein R-Ras: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Toxin B

Ras-related protein R-Ras

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