- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.34 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 1 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)
- 5 x NH4: AMMONIUM ION(Non-functional Binders)
NH4.2: 3 residues within 4Å:- Chain A: R.262, Y.454, V.457
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.262, A:R.262
- Water bridges: A:Y.454
NH4.9: 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
NH4.12: 3 residues within 4Å:- Chain A: S.306, M.316, T.338
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:S.306, A:T.338, A:T.338
NH4.17: 3 residues within 4Å:- Chain A: F.523, N.524, R.527
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.524, A:N.524
NH4.28: 3 residues within 4Å:- Chain A: K.380
- Chain B: D.37, P.38
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:K.380, A:K.380
- 7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.3: 4 residues within 4Å:- Chain A: N.238, D.239, N.242
- Ligands: EDO.5
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.239, A:N.242
EDO.4: 3 residues within 4Å:- Chain A: N.242, F.243
- Ligands: EDO.5
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.242
- Water bridges: A:E.244
EDO.5: 7 residues within 4Å:- Chain A: N.97, N.126, N.128, N.238, I.280
- Ligands: EDO.3, EDO.4
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:N.128, A:N.238
- Water bridges: A:N.128
EDO.7: 3 residues within 4Å:- Chain A: V.311, E.314, K.506
5 PLIP interactions:5 interactions with chain A- Water bridges: A:K.506, A:K.506, A:K.506, A:K.506, A:Q.511
EDO.25: 2 residues within 4Å:- Chain A: I.81, E.85
No protein-ligand interaction detected (PLIP)EDO.26: 7 residues within 4Å:- Chain B: F.113, P.114, V.115, H.143, V.144, A.145, A.167
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:F.113, B:V.115, B:A.145
EDO.27: 5 residues within 4Å:- Chain A: N.524
- Chain B: S.34, D.35, D.37
- Ligands: GDP.30
3 PLIP interactions:2 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:S.34, A:N.524
- Water bridges: B:Y.36
- 10 x ACT: ACETATE ION(Non-functional Binders)
ACT.6: 3 residues within 4Å:- Chain A: D.300, I.301, S.346
No protein-ligand interaction detected (PLIP)ACT.8: 5 residues within 4Å:- Chain A: Q.184, N.188, I.419, G.422
- Ligands: ACT.10
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:I.419
- Hydrogen bonds: A:Q.184, A:N.188
ACT.10: 6 residues within 4Å:- Chain A: Y.180, D.181, Q.184, G.422, N.423
- Ligands: ACT.8
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:Y.180, A:Q.184
ACT.11: 4 residues within 4Å:- Chain A: S.2, E.82, E.85, L.86
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:S.2, A:E.82
ACT.13: 3 residues within 4Å:- Chain A: T.140, K.216, Y.224
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:K.216
ACT.14: 1 residues within 4Å:- Chain A: V.80
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:V.80
ACT.15: 1 residues within 4Å:- Chain A: S.349
No protein-ligand interaction detected (PLIP)ACT.16: 3 residues within 4Å:- Chain A: H.294, P.295, D.296
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.296
- Salt bridges: A:H.294
ACT.22: 2 residues within 4Å:- Chain A: R.500, N.501
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.501
ACT.29: 2 residues within 4Å:- Chain B: D.158, E.159
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:D.158
- Hydrogen bonds: B:D.158
- Water bridges: B:R.154, B:D.158
- 1 x MN: MANGANESE (II) ION(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
MG.19: 5 residues within 4Å:- Chain A: D.286, V.287, D.288
- Ligands: UDP.1, MG.20
No protein-ligand interaction detected (PLIP)MG.20: 7 residues within 4Å:- Chain A: D.288, Q.515, N.518, L.520
- Ligands: UDP.1, MN.18, MG.19
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:Q.515, A:N.518, H2O.8
MG.21: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.24: 3 residues within 4Å:- Chain A: E.462
- Chain B: S.21
- Ligands: GDP.30
No protein-ligand interaction detected (PLIP)- 1 x GLC: alpha-D-glucopyranose(Non-covalent)
GLC.23: 13 residues within 4Å:- Chain A: A.266, D.270, R.273, D.286, N.385, Q.386, T.466, I.467, G.471, P.472, W.521
- Chain B: N.39
- Ligands: UDP.1
7 PLIP interactions:6 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:D.270, A:D.286, A:N.385, A:Q.386, A:W.521, B:N.39
- Salt bridges: A:R.273
- 1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)
GDP.30: 18 residues within 4Å:- Chain B: G.15, G.17, V.18, G.19, K.20, S.21, A.22, F.32, S.34, N.120, K.121, D.123, L.124, S.150, A.151, K.152
- Ligands: MG.24, EDO.27
19 PLIP interactions:19 interactions with chain B- Hydrogen bonds: B:G.17, B:V.18, B:G.19, B:K.20, B:S.21, B:A.22, B:S.34, B:N.120, B:K.121, B:K.121, B:S.150, B:A.151, B:K.152
- Water bridges: B:K.20, B:K.20
- Salt bridges: B:K.20, B:D.123
- pi-Stacking: B:F.32, B:F.32
- 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
AB
C
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.34 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 1 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)
- 5 x NH4: AMMONIUM ION(Non-functional Binders)
- 7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 10 x ACT: ACETATE ION(Non-functional Binders)
- 1 x MN: MANGANESE (II) ION(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
- 1 x GLC: alpha-D-glucopyranose(Non-covalent)
- 1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)
- 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
AB
C