- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- homo-15-mer
- Ligands
- 15 x DCW: DICYCLOHEXYLUREA(Non-covalent)
- 135 x CVM: CYMAL-4(Non-functional Binders)(Non-covalent)
CVM.2: 4 residues within 4Å:- Ligands: DCW.1, CVM.4, CVM.8, CVM.14
No protein-ligand interaction detected (PLIP)CVM.3: 3 residues within 4Å:- Chain A: V.74
- Ligands: CVM.9, CVM.149
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:V.74
CVM.4: 5 residues within 4Å:- Chain A: L.69
- Chain B: Y.67
- Ligands: CVM.2, CVM.9, CVM.14
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain B- Hydrophobic interactions: A:L.69, B:Y.67
CVM.5: 3 residues within 4Å:- Chain A: L.56
- Chain O: R.51, L.55
2 PLIP interactions:1 interactions with chain O, 1 interactions with chain A- Hydrophobic interactions: O:L.55, A:L.56
CVM.6: 9 residues within 4Å:- Chain A: S.3, N.4, L.5, A.8, A.9
- Chain B: L.5
- Chain O: S.3
- Ligands: CVM.11, CVM.134
4 PLIP interactions:3 interactions with chain A, 1 interactions with chain O- Hydrogen bonds: A:S.3, A:N.4, A:L.5, O:S.3
CVM.7: 8 residues within 4Å:- Chain A: A.63, I.66, Y.67
- Ligands: DCW.1, CVM.8, DCW.140, CVM.145, CVM.148
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:A.63, A:I.66, A:Y.67
CVM.8: 4 residues within 4Å:- Chain A: L.69, V.70
- Ligands: CVM.2, CVM.7
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:L.69, A:V.70
CVM.9: 5 residues within 4Å:- Chain A: F.77
- Chain B: V.74
- Ligands: CVM.3, CVM.4, CVM.18
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain B- Hydrophobic interactions: A:F.77, B:V.74
CVM.10: 3 residues within 4Å:- Chain A: L.55, A.59
- Ligands: CVM.12
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:L.55, A:A.59
CVM.11: 6 residues within 4Å:- Chain B: L.5, A.9, I.12
- Chain C: L.5
- Ligands: CVM.6, CVM.23
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:L.5, B:A.9, B:I.12
- Water bridges: B:L.5
CVM.12: 3 residues within 4Å:- Chain A: L.55
- Chain B: F.60
- Ligands: CVM.10
3 PLIP interactions:2 interactions with chain A, 1 interactions with chain B- Hydrophobic interactions: A:L.55, A:L.55, B:F.60
CVM.14: 7 residues within 4Å:- Chain B: A.63, I.66, Y.67
- Ligands: DCW.1, CVM.2, CVM.4, DCW.13
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:A.63, B:I.66, B:Y.67
CVM.15: 4 residues within 4Å:- Chain B: L.69, V.70, L.73
- Ligands: CVM.22
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:L.69, B:V.70, B:L.73
CVM.16: 5 residues within 4Å:- Chain B: F.77
- Ligands: CVM.17, CVM.18, CVM.26, CVM.27
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:F.77, B:F.77
CVM.17: 4 residues within 4Å:- Chain B: L.69
- Ligands: CVM.16, CVM.22, CVM.24
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:L.69
CVM.18: 5 residues within 4Å:- Chain B: L.73, F.77, A.78
- Ligands: CVM.9, CVM.16
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:L.73, B:F.77, B:F.77, B:A.78
CVM.19: 2 residues within 4Å:- Chain B: L.55, A.59
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:L.55, B:L.55, B:A.59
CVM.20: 3 residues within 4Å:- Chain B: L.55
- Chain C: L.56
- Ligands: CVM.30
No protein-ligand interaction detected (PLIP)CVM.22: 6 residues within 4Å:- Chain B: L.69
- Chain C: Y.67
- Ligands: DCW.13, CVM.15, CVM.17, CVM.24
2 PLIP interactions:1 interactions with chain C, 1 interactions with chain B- Hydrophobic interactions: C:Y.67, B:L.69
CVM.23: 10 residues within 4Å:- Chain B: S.3
- Chain C: S.3, N.4, L.5, A.8, A.9, I.12
- Chain D: L.5
- Ligands: CVM.11, CVM.31
5 PLIP interactions:4 interactions with chain C, 1 interactions with chain B- Hydrophobic interactions: C:A.8, C:I.12
- Hydrogen bonds: C:S.3, C:L.5, B:S.3
CVM.24: 6 residues within 4Å:- Chain C: A.63, Y.67
- Ligands: CVM.17, DCW.21, CVM.22, CVM.25
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:A.63, C:Y.67
CVM.25: 6 residues within 4Å:- Chain C: I.66
- Chain D: Y.67
- Ligands: DCW.21, CVM.24, CVM.28, CVM.32
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:I.66
CVM.26: 3 residues within 4Å:- Chain C: I.66, L.69
- Ligands: CVM.16
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:I.66, C:L.69
CVM.27: 4 residues within 4Å:- Chain C: L.73, F.77
- Ligands: CVM.16, CVM.29
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:L.73, C:F.77
CVM.28: 5 residues within 4Å:- Chain C: L.69
- Chain D: V.70
- Ligands: CVM.25, CVM.29, CVM.32
2 PLIP interactions:1 interactions with chain D, 1 interactions with chain C- Hydrophobic interactions: D:V.70, C:L.69
CVM.29: 3 residues within 4Å:- Chain C: F.77
- Ligands: CVM.27, CVM.28
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:F.77, C:F.77
CVM.30: 4 residues within 4Å:- Chain C: L.56, A.59
- Ligands: CVM.20, DCW.21
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:L.56, C:A.59
CVM.31: 10 residues within 4Å:- Chain C: S.3, N.4
- Chain D: N.4, L.5, A.8, A.9, I.12
- Chain E: L.5
- Ligands: CVM.23, CVM.34
5 PLIP interactions:2 interactions with chain C, 3 interactions with chain D- Hydrogen bonds: C:S.3, C:S.3, D:L.5
- Hydrophobic interactions: D:A.8, D:I.12
CVM.32: 6 residues within 4Å:- Chain D: A.63, I.66, Y.67
- Ligands: CVM.25, CVM.28, DCW.35
3 PLIP interactions:3 interactions with chain D- Hydrophobic interactions: D:A.63, D:I.66, D:Y.67
CVM.33: 2 residues within 4Å:- Chain C: L.55
- Ligands: DCW.21
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:L.55
CVM.34: 6 residues within 4Å:- Chain E: L.5, A.8, A.9
- Chain F: L.5
- Ligands: CVM.31, CVM.56
4 PLIP interactions:1 interactions with chain D, 2 interactions with chain E, 1 interactions with chain F- Water bridges: D:S.3
- Hydrophobic interactions: E:L.5, E:A.8, F:L.5
CVM.36: 2 residues within 4Å:- Chain D: L.73, F.77
2 PLIP interactions:2 interactions with chain D- Hydrophobic interactions: D:L.73, D:F.77
CVM.37: 3 residues within 4Å:- Chain D: F.77
- Ligands: CVM.43, CVM.47
1 PLIP interactions:1 interactions with chain D- Hydrophobic interactions: D:F.77
CVM.38: 6 residues within 4Å:- Chain C: R.51
- Chain D: G.52, L.55, L.56, A.59
- Ligands: CVM.39
2 PLIP interactions:2 interactions with chain D- Hydrophobic interactions: D:L.55, D:A.59
CVM.39: 4 residues within 4Å:- Chain D: L.55
- Chain E: L.56
- Ligands: CVM.38, CVM.50
3 PLIP interactions:1 interactions with chain E, 2 interactions with chain D- Hydrophobic interactions: E:L.56, D:L.55, D:L.55
CVM.41: 6 residues within 4Å:- Chain D: I.66
- Chain E: Y.67
- Ligands: DCW.35, CVM.42, CVM.43, CVM.44
2 PLIP interactions:1 interactions with chain E, 1 interactions with chain D- Hydrophobic interactions: E:Y.67, D:I.66
CVM.42: 4 residues within 4Å:- Chain D: I.66, V.70, L.73
- Ligands: CVM.41
3 PLIP interactions:3 interactions with chain D- Hydrophobic interactions: D:I.66, D:V.70, D:L.73
CVM.43: 6 residues within 4Å:- Chain D: L.69
- Chain E: Y.67, V.70
- Ligands: CVM.37, CVM.41, CVM.44
4 PLIP interactions:3 interactions with chain E, 1 interactions with chain D- Hydrophobic interactions: E:Y.67, E:Y.67, E:V.70, D:L.69
CVM.44: 7 residues within 4Å:- Chain E: A.63, I.66, Y.67
- Ligands: DCW.40, CVM.41, CVM.43, CVM.45
4 PLIP interactions:4 interactions with chain E- Hydrophobic interactions: E:A.63, E:I.66, E:I.66, E:Y.67
CVM.45: 6 residues within 4Å:- Chain E: I.66
- Chain F: Y.67
- Ligands: DCW.40, CVM.44, CVM.46, CVM.57
2 PLIP interactions:1 interactions with chain F, 1 interactions with chain E- Hydrophobic interactions: F:Y.67, E:I.66
CVM.46: 5 residues within 4Å:- Chain E: I.66, L.69, V.70, L.73
- Ligands: CVM.45
4 PLIP interactions:4 interactions with chain E- Hydrophobic interactions: E:I.66, E:L.69, E:V.70, E:L.73
CVM.47: 4 residues within 4Å:- Chain E: L.73, V.74, F.77
- Ligands: CVM.37
3 PLIP interactions:3 interactions with chain E- Hydrophobic interactions: E:L.73, E:V.74, E:F.77
CVM.48: 3 residues within 4Å:- Chain E: L.69
- Ligands: CVM.49, CVM.57
1 PLIP interactions:1 interactions with chain E- Hydrophobic interactions: E:L.69
CVM.49: 4 residues within 4Å:- Chain E: F.77
- Chain F: V.70
- Ligands: CVM.48, CVM.53
2 PLIP interactions:1 interactions with chain F, 1 interactions with chain E- Hydrophobic interactions: F:V.70, E:F.77
CVM.50: 4 residues within 4Å:- Chain E: G.52, L.55, A.59
- Ligands: CVM.39
3 PLIP interactions:3 interactions with chain E- Hydrophobic interactions: E:L.55, E:L.55, E:A.59
CVM.52: 4 residues within 4Å:- Ligands: DCW.51, CVM.54, CVM.58, CVM.64
No protein-ligand interaction detected (PLIP)CVM.53: 3 residues within 4Å:- Chain F: V.74
- Ligands: CVM.49, CVM.59
1 PLIP interactions:1 interactions with chain F- Hydrophobic interactions: F:V.74
CVM.54: 5 residues within 4Å:- Chain F: L.69
- Chain G: Y.67
- Ligands: CVM.52, CVM.59, CVM.64
2 PLIP interactions:1 interactions with chain G, 1 interactions with chain F- Hydrophobic interactions: G:Y.67, F:L.69
CVM.55: 3 residues within 4Å:- Chain E: R.51, L.55
- Chain F: L.56
2 PLIP interactions:1 interactions with chain F, 1 interactions with chain E- Hydrophobic interactions: F:L.56, E:L.55
CVM.56: 9 residues within 4Å:- Chain E: S.3
- Chain F: S.3, N.4, L.5, A.8, A.9
- Chain G: L.5
- Ligands: CVM.34, CVM.61
4 PLIP interactions:3 interactions with chain F, 1 interactions with chain E- Hydrogen bonds: F:S.3, F:N.4, F:L.5, E:S.3
CVM.57: 8 residues within 4Å:- Chain F: A.63, I.66, Y.67
- Ligands: DCW.40, CVM.45, CVM.48, DCW.51, CVM.58
3 PLIP interactions:3 interactions with chain F- Hydrophobic interactions: F:A.63, F:I.66, F:Y.67
CVM.58: 4 residues within 4Å:- Chain F: L.69, V.70
- Ligands: CVM.52, CVM.57
2 PLIP interactions:2 interactions with chain F- Hydrophobic interactions: F:L.69, F:V.70
CVM.59: 5 residues within 4Å:- Chain F: F.77
- Chain G: V.74
- Ligands: CVM.53, CVM.54, CVM.68
2 PLIP interactions:1 interactions with chain F, 1 interactions with chain G- Hydrophobic interactions: F:F.77, G:V.74
CVM.60: 3 residues within 4Å:- Chain F: L.55, A.59
- Ligands: CVM.62
2 PLIP interactions:2 interactions with chain F- Hydrophobic interactions: F:L.55, F:A.59
CVM.61: 6 residues within 4Å:- Chain G: L.5, A.9, I.12
- Chain H: L.5
- Ligands: CVM.56, CVM.73
4 PLIP interactions:4 interactions with chain G- Hydrophobic interactions: G:L.5, G:A.9, G:I.12
- Water bridges: G:L.5
CVM.62: 3 residues within 4Å:- Chain F: L.55
- Chain G: F.60
- Ligands: CVM.60
3 PLIP interactions:2 interactions with chain F, 1 interactions with chain G- Hydrophobic interactions: F:L.55, F:L.55, G:F.60
CVM.64: 7 residues within 4Å:- Chain G: A.63, I.66, Y.67
- Ligands: DCW.51, CVM.52, CVM.54, DCW.63
3 PLIP interactions:3 interactions with chain G- Hydrophobic interactions: G:A.63, G:I.66, G:Y.67
CVM.65: 4 residues within 4Å:- Chain G: L.69, V.70, L.73
- Ligands: CVM.72
3 PLIP interactions:3 interactions with chain G- Hydrophobic interactions: G:L.69, G:V.70, G:L.73
CVM.66: 5 residues within 4Å:- Chain G: F.77
- Ligands: CVM.67, CVM.68, CVM.76, CVM.77
2 PLIP interactions:2 interactions with chain G- Hydrophobic interactions: G:F.77, G:F.77
CVM.67: 4 residues within 4Å:- Chain G: L.69
- Ligands: CVM.66, CVM.72, CVM.74
1 PLIP interactions:1 interactions with chain G- Hydrophobic interactions: G:L.69
CVM.68: 5 residues within 4Å:- Chain G: L.73, F.77, A.78
- Ligands: CVM.59, CVM.66
4 PLIP interactions:4 interactions with chain G- Hydrophobic interactions: G:L.73, G:F.77, G:F.77, G:A.78
CVM.69: 2 residues within 4Å:- Chain G: L.55, A.59
3 PLIP interactions:3 interactions with chain G- Hydrophobic interactions: G:L.55, G:L.55, G:A.59
CVM.70: 3 residues within 4Å:- Chain G: L.55
- Chain H: L.56
- Ligands: CVM.80
No protein-ligand interaction detected (PLIP)CVM.72: 6 residues within 4Å:- Chain G: L.69
- Chain H: Y.67
- Ligands: DCW.63, CVM.65, CVM.67, CVM.74
2 PLIP interactions:1 interactions with chain H, 1 interactions with chain G- Hydrophobic interactions: H:Y.67, G:L.69
CVM.73: 10 residues within 4Å:- Chain G: S.3
- Chain H: S.3, N.4, L.5, A.8, A.9, I.12
- Chain I: L.5
- Ligands: CVM.61, CVM.81
5 PLIP interactions:1 interactions with chain G, 4 interactions with chain H- Hydrogen bonds: G:S.3, H:S.3, H:L.5
- Hydrophobic interactions: H:A.8, H:I.12
CVM.74: 6 residues within 4Å:- Chain H: A.63, Y.67
- Ligands: CVM.67, DCW.71, CVM.72, CVM.75
2 PLIP interactions:2 interactions with chain H- Hydrophobic interactions: H:A.63, H:Y.67
CVM.75: