- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.88 Å
- Oligo State
- hetero-6-6-6-6-mer
- Ligands
- 6 x SIA: N-acetyl-alpha-neuraminic acid(Non-covalent)
- 12 x HEZ: HEXANE-1,6-DIOL(Non-covalent)
HEZ.2: 6 residues within 4Å:- Chain A: N.154, Y.189, S.191
- Chain E: N.154, G.190
- Ligands: HEZ.19
4 PLIP interactions:3 interactions with chain A, 1 interactions with chain G- Hydrophobic interactions: A:N.154
- Hydrogen bonds: A:S.191
- Water bridges: A:R.153, G:S.11
HEZ.3: 4 residues within 4Å:- Chain A: Y.230, T.235, E.284
- Chain B: T.140
4 PLIP interactions:3 interactions with chain A, 1 interactions with chain B- Hydrophobic interactions: A:Y.230
- Hydrogen bonds: A:E.284
- Water bridges: A:Y.230, B:T.140
HEZ.19: 4 residues within 4Å:- Chain E: N.154, Y.189, S.191
- Ligands: HEZ.2
2 PLIP interactions:2 interactions with chain E- Hydrophobic interactions: E:N.154
- Hydrogen bonds: E:S.191
HEZ.20: 4 residues within 4Å:- Chain E: Y.230, T.235, E.284
- Chain F: T.140
4 PLIP interactions:3 interactions with chain E, 1 interactions with chain F- Hydrophobic interactions: E:Y.230
- Hydrogen bonds: E:E.284
- Water bridges: E:Y.230, F:T.140
HEZ.36: 4 residues within 4Å:- Chain I: N.154, Y.189, S.191
- Ligands: HEZ.53
2 PLIP interactions:2 interactions with chain I- Hydrophobic interactions: I:N.154
- Hydrogen bonds: I:S.191
HEZ.37: 4 residues within 4Å:- Chain I: Y.230, T.235, E.284
- Chain J: T.140
4 PLIP interactions:1 interactions with chain J, 3 interactions with chain I- Water bridges: J:T.140, I:Y.230
- Hydrophobic interactions: I:Y.230
- Hydrogen bonds: I:E.284
HEZ.53: 6 residues within 4Å:- Chain I: N.154, G.190
- Chain M: N.154, Y.189, S.191
- Ligands: HEZ.36
4 PLIP interactions:3 interactions with chain M, 1 interactions with chain K- Hydrophobic interactions: M:N.154
- Hydrogen bonds: M:S.191
- Water bridges: M:R.153, K:S.11
HEZ.54: 4 residues within 4Å:- Chain M: Y.230, T.235, E.284
- Chain N: T.140
4 PLIP interactions:3 interactions with chain M, 1 interactions with chain N- Hydrophobic interactions: M:Y.230
- Hydrogen bonds: M:E.284
- Water bridges: M:Y.230, N:T.140
HEZ.70: 6 residues within 4Å:- Chain Q: N.154, Y.189, S.191
- Chain U: N.154, G.190
- Ligands: HEZ.87
4 PLIP interactions:3 interactions with chain Q, 1 interactions with chain W- Hydrophobic interactions: Q:N.154
- Hydrogen bonds: Q:S.191
- Water bridges: Q:R.153, W:S.11
HEZ.71: 4 residues within 4Å:- Chain Q: Y.230, T.235, E.284
- Chain R: T.140
4 PLIP interactions:1 interactions with chain R, 3 interactions with chain Q- Water bridges: R:T.140, Q:Y.230
- Hydrophobic interactions: Q:Y.230
- Hydrogen bonds: Q:E.284
HEZ.87: 4 residues within 4Å:- Chain U: N.154, Y.189, S.191
- Ligands: HEZ.70
2 PLIP interactions:2 interactions with chain U- Hydrophobic interactions: U:N.154
- Hydrogen bonds: U:S.191
HEZ.88: 4 residues within 4Å:- Chain U: Y.230, T.235, E.284
- Chain V: T.140
3 PLIP interactions:1 interactions with chain V, 2 interactions with chain U- Water bridges: V:T.140, U:Y.230
- Hydrophobic interactions: U:Y.230
- 30 x CA: CALCIUM ION(Non-covalent)
CA.4: 4 residues within 4Å:- Chain A: T.33, S.34, S.58, I.61
6 PLIP interactions:4 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:T.33, A:S.34, A:S.58, A:I.61, H2O.10, H2O.104
CA.5: 4 residues within 4Å:- Chain A: V.41, L.44
- Chain D: K.63, A.65
5 PLIP interactions:1 interactions with chain A, 2 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: A:L.44, D:K.63, D:A.65, H2O.6, H2O.6
CA.6: 4 residues within 4Å:- Chain A: T.26, A.27, S.29, N.68
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:T.26, A:A.27, A:S.29, A:N.68
CA.11: 1 residues within 4Å:- Chain B: E.55
3 PLIP interactions:1 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:E.55, H2O.16, H2O.20
CA.14: 3 residues within 4Å:- Chain C: T.4
- Chain G: T.4
- Ligands: CA.31
No protein-ligand interaction detected (PLIP)CA.21: 4 residues within 4Å:- Chain E: T.33, S.34, S.58, I.61
5 PLIP interactions:4 interactions with chain E, 1 Ligand-Water interactions- Metal complexes: E:T.33, E:S.34, E:S.58, E:I.61, H2O.40
CA.22: 4 residues within 4Å:- Chain E: V.41, L.44
- Chain H: K.63, A.65
5 PLIP interactions:2 interactions with chain H, 1 interactions with chain E, 2 Ligand-Water interactions- Metal complexes: H:K.63, H:A.65, E:L.44, H2O.37, H2O.37
CA.23: 4 residues within 4Å:- Chain E: T.26, A.27, S.29, N.68
4 PLIP interactions:4 interactions with chain E- Metal complexes: E:T.26, E:A.27, E:S.29, E:N.68
CA.28: 1 residues within 4Å:- Chain F: E.55
3 PLIP interactions:1 interactions with chain F, 2 Ligand-Water interactions- Metal complexes: F:E.55, H2O.46, H2O.50
CA.31: 3 residues within 4Å:- Chain C: T.4
- Chain G: T.4
- Ligands: CA.14
No protein-ligand interaction detected (PLIP)CA.38: 4 residues within 4Å:- Chain I: T.33, S.34, S.58, I.61
5 PLIP interactions:4 interactions with chain I, 1 Ligand-Water interactions- Metal complexes: I:T.33, I:S.34, I:S.58, I:I.61, H2O.71
CA.39: 4 residues within 4Å:- Chain I: V.41, L.44
- Chain L: K.63, A.65
5 PLIP interactions:1 interactions with chain I, 2 interactions with chain L, 2 Ligand-Water interactions- Metal complexes: I:L.44, L:K.63, L:A.65, H2O.67, H2O.67
CA.40: 4 residues within 4Å:- Chain I: T.26, A.27, S.29, N.68
4 PLIP interactions:4 interactions with chain I- Metal complexes: I:T.26, I:A.27, I:S.29, I:N.68
CA.45: 1 residues within 4Å:- Chain J: E.55
3 PLIP interactions:1 interactions with chain J, 2 Ligand-Water interactions- Metal complexes: J:E.55, H2O.77, H2O.81
CA.48: 3 residues within 4Å:- Chain K: T.4
- Chain O: T.4
- Ligands: CA.65
No protein-ligand interaction detected (PLIP)CA.55: 4 residues within 4Å:- Chain M: T.33, S.34, S.58, I.61
6 PLIP interactions:4 interactions with chain M, 2 Ligand-Water interactions- Metal complexes: M:T.33, M:S.34, M:S.58, M:I.61, H2O.101, H2O.134
CA.56: 4 residues within 4Å:- Chain M: V.41, L.44
- Chain P: K.63, A.65
5 PLIP interactions:2 interactions with chain P, 1 interactions with chain M, 2 Ligand-Water interactions- Metal complexes: P:K.63, P:A.65, M:L.44, H2O.98, H2O.98
CA.57: 4 residues within 4Å:- Chain M: T.26, A.27, S.29, N.68
4 PLIP interactions:4 interactions with chain M- Metal complexes: M:T.26, M:A.27, M:S.29, M:N.68
CA.62: 1 residues within 4Å:- Chain N: E.55
3 PLIP interactions:1 interactions with chain N, 2 Ligand-Water interactions- Metal complexes: N:E.55, H2O.107, H2O.111
CA.65: 3 residues within 4Å:- Chain K: T.4
- Chain O: T.4
- Ligands: CA.48
No protein-ligand interaction detected (PLIP)CA.72: 4 residues within 4Å:- Chain Q: T.33, S.34, S.58, I.61
6 PLIP interactions:4 interactions with chain Q, 2 Ligand-Water interactions- Metal complexes: Q:T.33, Q:S.34, Q:S.58, Q:I.61, H2O.12, H2O.132
CA.73: 4 residues within 4Å:- Chain Q: V.41, L.44
- Chain T: K.63, A.65
5 PLIP interactions:2 interactions with chain T, 1 interactions with chain Q, 2 Ligand-Water interactions- Metal complexes: T:K.63, T:A.65, Q:L.44, H2O.128, H2O.128
CA.74: 4 residues within 4Å:- Chain Q: T.26, A.27, S.29, N.68
4 PLIP interactions:4 interactions with chain Q- Metal complexes: Q:T.26, Q:A.27, Q:S.29, Q:N.68
CA.79: 1 residues within 4Å:- Chain R: E.55
3 PLIP interactions:1 interactions with chain R, 2 Ligand-Water interactions- Metal complexes: R:E.55, H2O.138, H2O.142
CA.82: 3 residues within 4Å:- Chain S: T.4
- Chain W: T.4
- Ligands: CA.99
No protein-ligand interaction detected (PLIP)CA.89: 4 residues within 4Å:- Chain U: T.33, S.34, S.58, I.61
5 PLIP interactions:4 interactions with chain U, 1 Ligand-Water interactions- Metal complexes: U:T.33, U:S.34, U:S.58, U:I.61, H2O.162
CA.90: 4 residues within 4Å:- Chain U: V.41, L.44
- Chain X: K.63, A.65
5 PLIP interactions:1 interactions with chain U, 2 interactions with chain X, 2 Ligand-Water interactions- Metal complexes: U:L.44, X:K.63, X:A.65, H2O.159, H2O.159
CA.91: 4 residues within 4Å:- Chain U: T.26, A.27, S.29, N.68
4 PLIP interactions:4 interactions with chain U- Metal complexes: U:T.26, U:A.27, U:S.29, U:N.68
CA.96: 1 residues within 4Å:- Chain V: E.55
3 PLIP interactions:1 interactions with chain V, 2 Ligand-Water interactions- Metal complexes: V:E.55, H2O.168, H2O.172
CA.99: 3 residues within 4Å:- Chain S: T.4
- Chain W: T.4
- Ligands: CA.82
No protein-ligand interaction detected (PLIP)- 42 x CL: CHLORIDE ION(Non-functional Binders)
CL.7: 5 residues within 4Å:- Chain A: N.248, E.249
- Chain E: T.141, E.142, K.258
Ligand excluded by PLIPCL.8: 2 residues within 4Å:- Chain A: R.245
- Chain E: R.260
Ligand excluded by PLIPCL.9: 4 residues within 4Å:- Chain A: V.299, E.300, T.304
- Chain C: K.92
Ligand excluded by PLIPCL.10: 5 residues within 4Å:- Chain A: K.220, D.221
- Chain B: A.269, T.270, Q.271
Ligand excluded by PLIPCL.13: 3 residues within 4Å:- Chain B: K.87, G.151, E.152
Ligand excluded by PLIPCL.15: 2 residues within 4Å:- Chain C: T.59, G.60
Ligand excluded by PLIPCL.16: 2 residues within 4Å:- Chain C: F.19, Q.20
Ligand excluded by PLIPCL.24: 2 residues within 4Å:- Chain E: N.248, E.249
Ligand excluded by PLIPCL.25: 1 residues within 4Å:- Chain E: R.245
Ligand excluded by PLIPCL.26: 4 residues within 4Å:- Chain E: V.299, E.300, T.304
- Chain G: K.92
Ligand excluded by PLIPCL.27: 5 residues within 4Å:- Chain E: K.220, D.221
- Chain F: A.269, T.270, Q.271
Ligand excluded by PLIPCL.30: 3 residues within 4Å:- Chain F: K.87, G.151, E.152
Ligand excluded by PLIPCL.32: 2 residues within 4Å:- Chain G: T.59, G.60
Ligand excluded by PLIPCL.33: 2 residues within 4Å:- Chain G: F.19, Q.20
Ligand excluded by PLIPCL.41: 2 residues within 4Å:- Chain I: N.248, E.249
Ligand excluded by PLIPCL.42: 1 residues within 4Å:- Chain I: R.245
Ligand excluded by PLIPCL.43: 4 residues within 4Å:- Chain I: V.299, E.300, T.304
- Chain K: K.92
Ligand excluded by PLIPCL.44: 5 residues within 4Å:- Chain I: K.220, D.221
- Chain J: A.269, T.270, Q.271
Ligand excluded by PLIPCL.47: 3 residues within 4Å:- Chain J: K.87, G.151, E.152
Ligand excluded by PLIPCL.49: 2 residues within 4Å:- Chain K: T.59, G.60
Ligand excluded by PLIPCL.50: 2 residues within 4Å:- Chain K: F.19, Q.20
Ligand excluded by PLIPCL.58: 5 residues within 4Å:- Chain I: T.141, E.142, K.258
- Chain M: N.248, E.249
Ligand excluded by PLIPCL.59: 2 residues within 4Å:- Chain I: R.260
- Chain M: R.245
Ligand excluded by PLIPCL.60: 4 residues within 4Å:- Chain M: V.299, E.300, T.304
- Chain O: K.92
Ligand excluded by PLIPCL.61: 5 residues within 4Å:- Chain M: K.220, D.221
- Chain N: A.269, T.270, Q.271
Ligand excluded by PLIPCL.64: 3 residues within 4Å:- Chain N: K.87, G.151, E.152
Ligand excluded by PLIPCL.66: 2 residues within 4Å:- Chain O: T.59, G.60
Ligand excluded by PLIPCL.67: 2 residues within 4Å:- Chain O: F.19, Q.20
Ligand excluded by PLIPCL.75: 5 residues within 4Å:- Chain Q: N.248, E.249
- Chain U: T.141, E.142, K.258
Ligand excluded by PLIPCL.76: 2 residues within 4Å:- Chain Q: R.245
- Chain U: R.260
Ligand excluded by PLIPCL.77: 4 residues within 4Å:- Chain Q: V.299, E.300, T.304
- Chain S: K.92
Ligand excluded by PLIPCL.78: 5 residues within 4Å:- Chain Q: K.220, D.221
- Chain R: A.269, T.270, Q.271
Ligand excluded by PLIPCL.81: 3 residues within 4Å:- Chain R: K.87, G.151, E.152
Ligand excluded by PLIPCL.83: 2 residues within 4Å:- Chain S: T.59, G.60
Ligand excluded by PLIPCL.84: 2 residues within 4Å:- Chain S: F.19, Q.20
Ligand excluded by PLIPCL.92: 2 residues within 4Å:- Chain U: N.248, E.249
Ligand excluded by PLIPCL.93: 1 residues within 4Å:- Chain U: R.245
Ligand excluded by PLIPCL.94: 4 residues within 4Å:- Chain U: V.299, E.300, T.304
- Chain W: K.92
Ligand excluded by PLIPCL.95: 5 residues within 4Å:- Chain U: K.220, D.221
- Chain V: A.269, T.270, Q.271
Ligand excluded by PLIPCL.98: 3 residues within 4Å:- Chain V: K.87, G.151, E.152
Ligand excluded by PLIPCL.100: 2 residues within 4Å:- Chain W: T.59, G.60
Ligand excluded by PLIPCL.101: 2 residues within 4Å:- Chain W: F.19, Q.20
Ligand excluded by PLIP- 6 x MG: MAGNESIUM ION(Non-covalent)
MG.12: 2 residues within 4Å:- Chain B: E.152
- Chain S: K.145
6 PLIP interactions:1 interactions with chain B, 5 Ligand-Water interactions- Metal complexes: B:E.152, H2O.15, H2O.17, H2O.18, H2O.20, H2O.144
MG.29: 1 residues within 4Å:- Chain F: E.152
5 PLIP interactions:1 interactions with chain F, 4 Ligand-Water interactions- Metal complexes: F:E.152, H2O.45, H2O.48, H2O.48, H2O.50
MG.46: 1 residues within 4Å:- Chain J: E.152
5 PLIP interactions:1 interactions with chain J, 4 Ligand-Water interactions- Metal complexes: J:E.152, H2O.76, H2O.78, H2O.79, H2O.81
MG.63: 2 residues within 4Å:- Chain C: K.145
- Chain N: E.152
6 PLIP interactions:1 interactions with chain N, 5 Ligand-Water interactions- Metal complexes: N:E.152, H2O.22, H2O.106, H2O.109, H2O.109, H2O.111
MG.80: 2 residues within 4Å:- Chain O: K.145
- Chain R: E.152
6 PLIP interactions:1 interactions with chain R, 5 Ligand-Water interactions- Metal complexes: R:E.152, H2O.114, H2O.137, H2O.139, H2O.140, H2O.142
MG.97: 1 residues within 4Å:- Chain V: E.152
5 PLIP interactions:1 interactions with chain V, 4 Ligand-Water interactions- Metal complexes: V:E.152, H2O.167, H2O.170, H2O.170, H2O.172
- 6 x MYR: MYRISTIC ACID(Covalent)
MYR.17: 4 residues within 4Å:- Chain D: G.2, A.3
- Chain H: V.5, T.28
No protein-ligand interaction detected (PLIP)MYR.34: 2 residues within 4Å:- Chain H: G.2, A.3
No protein-ligand interaction detected (PLIP)MYR.51: 2 residues within 4Å:- Chain L: G.2, A.3
No protein-ligand interaction detected (PLIP)MYR.68: 4 residues within 4Å:- Chain L: V.5, T.28
- Chain P: G.2, A.3
1 PLIP interactions:1 interactions with chain L- Hydrogen bonds: L:T.28
MYR.85: 4 residues within 4Å:- Chain T: G.2, A.3
- Chain X: V.5, T.28
No protein-ligand interaction detected (PLIP)MYR.102: 2 residues within 4Å:- Chain X: G.2, A.3
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zocher, G. et al., A sialic Acid binding site in a human picornavirus. Plos Pathog. (2014)
- Release Date
- 2014-11-05
- Peptides
- Coxsackievirus capsid protein VP1: AEIMQU
Coxsackievirus capsid protein VP2: BFJNRV
Coxsackievirus capsid protein VP3: CGKOSW
Coxsackievirus capsid protein VP4: DHLPTX - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
1E
1I
1M
1Q
1U
1B
2F
2J
2N
2R
2V
2C
3G
3K
3O
3S
3W
3D
4H
4L
4P
4T
4X
4
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.88 Å
- Oligo State
- hetero-6-6-6-6-mer
- Ligands
- 6 x SIA: N-acetyl-alpha-neuraminic acid(Non-covalent)
- 12 x HEZ: HEXANE-1,6-DIOL(Non-covalent)
- 30 x CA: CALCIUM ION(Non-covalent)
- 42 x CL: CHLORIDE ION(Non-functional Binders)
- 6 x MG: MAGNESIUM ION(Non-covalent)
- 6 x MYR: MYRISTIC ACID(Covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zocher, G. et al., A sialic Acid binding site in a human picornavirus. Plos Pathog. (2014)
- Release Date
- 2014-11-05
- Peptides
- Coxsackievirus capsid protein VP1: AEIMQU
Coxsackievirus capsid protein VP2: BFJNRV
Coxsackievirus capsid protein VP3: CGKOSW
Coxsackievirus capsid protein VP4: DHLPTX - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
1E
1I
1M
1Q
1U
1B
2F
2J
2N
2R
2V
2C
3G
3K
3O
3S
3W
3D
4H
4L
4P
4T
4X
4