SMTL ID : 7s0y.1

Structures of TcdB in complex with Cdc42

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

hetero-1-1-mer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: D.290, E.517 Ligands: UDP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.290, A:E.517, H2O.1, H2O.1

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

UDP.2: 18 residues within 4Å: Chain A: V.103, W.104, I.105, N.141, L.267, A.268, S.271, R.275, Y.286, D.288, V.289, D.290, E.517, S.520, L.521, W.522 Chain B: N.36 Ligands: MN.1 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.521 Hydrogen bonds: A:V.103, A:I.105, A:I.105, A:N.141, A:S.271, A:R.275, A:Y.286, A:V.289, A:L.521, B:N.36 Water bridges: A:V.103, A:D.288, A:D.288, A:A.519 pi-Stacking: A:W.104

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: N.240, D.241, N.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.240, A:D.241, A:N.244 SO4.4: 6 residues within 4Å: Chain A: F.379, N.380, S.381, K.382, R.501, K.507 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.381, A:K.382 Salt bridges: A:R.501, A:K.507 SO4.5: 2 residues within 4Å: Chain A: V.129, S.238 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.121 SO4.6: 7 residues within 4Å: Chain A: D.444, Q.481, K.487, G.489, S.490, M.491, N.492 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.481, A:M.491, A:N.492 Salt bridges: A:K.487 SO4.7: 3 residues within 4Å: Chain A: N.110, D.111, T.112 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.110, A:D.111, A:T.112, A:T.112 SO4.8: 2 residues within 4Å: Chain A: N.442, A.443 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.443 SO4.9: 4 residues within 4Å: Chain A: Y.328, S.356, D.357, K.358 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.328, A:K.358 SO4.10: 4 residues within 4Å: Chain A: T.64, Y.65, K.66, K.67 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.66, A:K.67 SO4.11: 3 residues within 4Å: Chain A: Q.296, S.363, S.364 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.296, A:Q.296, A:S.364 SO4.14: 2 residues within 4Å: Chain B: Q.62, E.63 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.63, A:R.175 SO4.15: 4 residues within 4Å: Chain B: S.87, P.88, S.89, Q.135 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.87, B:S.89, B:S.89, B:Q.135

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

GDP.12: 16 residues within 4Å: Chain B: D.12, G.13, A.14, V.15, G.16, K.17, T.18, C.19, F.29, Q.117, D.119, L.120, S.159, A.160, L.161 Ligands: MG.13 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:D.12, B:A.14, B:V.15, B:G.16, B:G.16, B:K.17, B:T.18, B:C.19, B:Q.117, B:Q.117, B:S.159, B:A.160, B:L.161 Water bridges: B:T.18, B:T.18, B:T.18 Salt bridges: B:K.17, B:D.119 pi-Stacking: B:F.29

1 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 4 residues within 4Å: Chain A: D.463 Chain B: T.18, D.58 Ligands: GDP.12 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.18, H2O.1, H2O.1, H2O.1, H2O.1

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
Cell division control protein 42 homolog: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Toxin B

Cell division control protein 42 homolog