- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-12-mer
- Ligands
- 12 x ZN: ZINC ION(Non-covalent)
- 12 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)
SAH.2: 13 residues within 4Å:- Chain A: G.65, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156
- Ligands: YG4.3
15 PLIP interactions:15 interactions with chain A- Hydrogen bonds: A:G.65, A:G.65, A:R.85, A:S.86, A:D.89, A:R.92, A:D.138, A:D.138
- Water bridges: A:R.41, A:A.67, A:A.67, A:Q.151, A:D.152
- Salt bridges: A:R.70, A:R.92
SAH.7: 13 residues within 4Å:- Chain B: G.65, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156
- Ligands: YG4.8
13 PLIP interactions:13 interactions with chain B- Hydrogen bonds: B:G.65, B:G.65, B:R.85, B:S.86, B:D.89, B:R.92, B:D.138, B:D.138
- Water bridges: B:R.41, B:A.67, B:Q.151
- Salt bridges: B:R.70, B:R.92
SAH.11: 13 residues within 4Å:- Chain C: G.65, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156
- Ligands: YG4.12
13 PLIP interactions:13 interactions with chain C- Hydrogen bonds: C:G.65, C:G.65, C:R.85, C:S.86, C:D.89, C:R.92, C:D.138, C:D.138
- Water bridges: C:R.41, C:A.67, C:Q.151
- Salt bridges: C:R.70, C:R.92
SAH.15: 13 residues within 4Å:- Chain D: G.65, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156
- Ligands: YG4.16
15 PLIP interactions:15 interactions with chain D- Hydrogen bonds: D:G.65, D:G.65, D:R.85, D:S.86, D:D.89, D:R.92, D:D.138, D:D.138
- Water bridges: D:R.41, D:A.67, D:A.67, D:Q.151, D:D.152
- Salt bridges: D:R.70, D:R.92
SAH.19: 13 residues within 4Å:- Chain E: G.65, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156
- Ligands: YG4.20
13 PLIP interactions:13 interactions with chain E- Hydrogen bonds: E:G.65, E:G.65, E:R.85, E:S.86, E:D.89, E:R.92, E:D.138, E:D.138
- Water bridges: E:R.41, E:A.67, E:Q.151
- Salt bridges: E:R.70, E:R.92
SAH.23: 13 residues within 4Å:- Chain F: G.65, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156
- Ligands: YG4.24
13 PLIP interactions:13 interactions with chain F- Hydrogen bonds: F:G.65, F:G.65, F:R.85, F:S.86, F:D.89, F:R.92, F:D.138, F:D.138
- Water bridges: F:R.41, F:A.67, F:Q.151
- Salt bridges: F:R.70, F:R.92
SAH.27: 13 residues within 4Å:- Chain G: G.65, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156
- Ligands: YG4.28
15 PLIP interactions:15 interactions with chain G- Hydrogen bonds: G:G.65, G:G.65, G:R.85, G:S.86, G:D.89, G:R.92, G:D.138, G:D.138
- Water bridges: G:R.41, G:A.67, G:A.67, G:Q.151, G:D.152
- Salt bridges: G:R.70, G:R.92
SAH.31: 13 residues within 4Å:- Chain H: G.65, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156
- Ligands: YG4.32
13 PLIP interactions:13 interactions with chain H- Hydrogen bonds: H:G.65, H:G.65, H:R.85, H:S.86, H:D.89, H:R.92, H:D.138, H:D.138
- Water bridges: H:R.41, H:A.67, H:Q.151
- Salt bridges: H:R.70, H:R.92
SAH.35: 13 residues within 4Å:- Chain I: G.65, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156
- Ligands: YG4.36
13 PLIP interactions:13 interactions with chain I- Hydrogen bonds: I:G.65, I:G.65, I:R.85, I:S.86, I:D.89, I:R.92, I:D.138, I:D.138
- Water bridges: I:R.41, I:A.67, I:Q.151
- Salt bridges: I:R.70, I:R.92
SAH.39: 13 residues within 4Å:- Chain J: G.65, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156
- Ligands: YG4.40
15 PLIP interactions:15 interactions with chain J- Hydrogen bonds: J:G.65, J:G.65, J:R.85, J:S.86, J:D.89, J:R.92, J:D.138, J:D.138
- Water bridges: J:R.41, J:A.67, J:A.67, J:Q.151, J:D.152
- Salt bridges: J:R.70, J:R.92
SAH.43: 13 residues within 4Å:- Chain K: G.65, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156
- Ligands: YG4.44
13 PLIP interactions:13 interactions with chain K- Hydrogen bonds: K:G.65, K:G.65, K:R.85, K:S.86, K:D.89, K:R.92, K:D.138, K:D.138
- Water bridges: K:R.41, K:A.67, K:Q.151
- Salt bridges: K:R.70, K:R.92
SAH.47: 13 residues within 4Å:- Chain L: G.65, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156
- Ligands: YG4.48
13 PLIP interactions:13 interactions with chain L- Hydrogen bonds: L:G.65, L:G.65, L:R.85, L:S.86, L:D.89, L:R.92, L:D.138, L:D.138
- Water bridges: L:R.41, L:A.67, L:Q.151
- Salt bridges: L:R.70, L:R.92
- 12 x YG4: [(2~{R},3~{R},4~{R},5~{R})-5-(6-azanyl-7,8-dihydropurin-9-yl)-2-[[[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-4-methoxy-oxolan-3-yl] [(2~{R},3~{S},4~{R},5~{S})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate(Non-covalent)
YG4.3: 19 residues within 4Å:- Chain A: T.33, N.35, A.40, R.41, R.70, K.99, D.152, Y.154, F.241, T.246, Y.248, E.250, Y.285
- Chain B: E.54, D.277, V.279, R.289
- Ligands: SAH.2, MG.5
19 PLIP interactions:14 interactions with chain A, 5 interactions with chain B- Hydrogen bonds: A:N.35, A:N.35, A:R.41, A:N.95, A:D.152, A:Y.248, A:Y.248, A:Y.285, B:D.277, B:V.279
- Salt bridges: A:R.41, A:R.70, A:K.99, A:E.250
- pi-Stacking: A:Y.248, A:Y.248
- Water bridges: B:R.275, B:R.275
- pi-Cation interactions: B:R.289
YG4.8: 20 residues within 4Å:- Chain B: T.33, N.35, A.40, R.41, R.70, N.95, K.99, D.152, Y.154, F.241, T.246, Y.248, E.250, Y.285
- Chain C: E.54, D.277, V.279, R.289
- Ligands: SAH.7, MG.9
23 PLIP interactions:17 interactions with chain B, 6 interactions with chain C- Hydrogen bonds: B:N.35, B:N.35, B:R.41, B:N.95, B:D.152, B:Y.248, B:Y.248, B:Y.285, C:D.277, C:V.279, C:R.289
- Water bridges: B:N.35, B:D.36, B:D.36, C:R.275, C:R.275
- Salt bridges: B:R.41, B:R.70, B:K.99, B:E.250
- pi-Stacking: B:Y.248, B:Y.248
- pi-Cation interactions: C:R.289
YG4.12: 19 residues within 4Å:- Chain C: T.33, N.35, A.40, R.41, R.70, N.95, K.99, D.152, Y.154, T.246, Y.248, E.250, Y.285
- Chain D: E.54, D.277, V.279, R.289
- Ligands: SAH.11, MG.13
21 PLIP interactions:15 interactions with chain C, 6 interactions with chain D- Hydrogen bonds: C:N.35, C:N.35, C:R.41, C:R.41, C:N.95, C:D.152, C:Y.248, C:Y.248, C:Y.285, D:D.277, D:V.279, D:R.289
- Salt bridges: C:R.41, C:R.70, C:K.99, C:E.250
- pi-Stacking: C:Y.248, C:Y.248
- Water bridges: D:R.275, D:R.275
- pi-Cation interactions: D:R.289
YG4.16: 19 residues within 4Å:- Chain D: T.33, N.35, A.40, R.41, R.70, K.99, D.152, Y.154, F.241, T.246, Y.248, E.250, Y.285
- Chain E: E.54, D.277, V.279, R.289
- Ligands: SAH.15, MG.17
19 PLIP interactions:14 interactions with chain D, 5 interactions with chain E- Hydrogen bonds: D:N.35, D:N.35, D:R.41, D:N.95, D:D.152, D:Y.248, D:Y.248, D:Y.285, E:D.277, E:V.279
- Salt bridges: D:R.41, D:R.70, D:K.99, D:E.250
- pi-Stacking: D:Y.248, D:Y.248
- Water bridges: E:R.275, E:R.275
- pi-Cation interactions: E:R.289
YG4.20: 19 residues within 4Å:- Chain E: T.33, N.35, A.40, R.41, R.70, K.99, D.152, Y.154, F.241, T.246, Y.248, E.250, Y.285
- Chain F: E.54, D.277, V.279, R.289
- Ligands: SAH.19, MG.21
23 PLIP interactions:17 interactions with chain E, 6 interactions with chain F- Hydrogen bonds: E:N.35, E:N.35, E:R.41, E:N.95, E:D.152, E:Y.248, E:Y.248, E:Y.285, F:D.277, F:V.279, F:R.289
- Water bridges: E:N.35, E:D.36, E:D.36, F:R.275, F:R.275
- Salt bridges: E:R.41, E:R.70, E:K.99, E:E.250
- pi-Stacking: E:Y.248, E:Y.248
- pi-Cation interactions: F:R.289
YG4.24: 19 residues within 4Å:- Chain F: T.33, N.35, A.40, R.41, R.70, N.95, K.99, D.152, Y.154, T.246, Y.248, E.250, Y.285
- Chain G: E.54, D.277, V.279, R.289
- Ligands: SAH.23, MG.25
21 PLIP interactions:15 interactions with chain F, 6 interactions with chain G- Hydrogen bonds: F:N.35, F:N.35, F:R.41, F:R.41, F:N.95, F:D.152, F:Y.248, F:Y.248, F:Y.285, G:D.277, G:V.279, G:R.289
- Salt bridges: F:R.41, F:R.70, F:K.99, F:E.250
- pi-Stacking: F:Y.248, F:Y.248
- Water bridges: G:R.275, G:R.275
- pi-Cation interactions: G:R.289
YG4.28: 19 residues within 4Å:- Chain G: N.35, A.40, R.41, R.70, N.95, K.99, D.152, Y.154, F.241, T.246, Y.248, E.250, Y.285
- Chain H: E.54, D.277, V.279, R.289
- Ligands: SAH.27, MG.29
18 PLIP interactions:4 interactions with chain H, 14 interactions with chain G- Hydrogen bonds: H:D.277, H:V.279, G:N.35, G:N.35, G:R.41, G:N.95, G:D.152, G:Y.248, G:Y.248, G:Y.285
- Water bridges: H:R.275
- pi-Cation interactions: H:R.289
- Salt bridges: G:R.41, G:R.70, G:K.99, G:E.250
- pi-Stacking: G:Y.248, G:Y.248
YG4.32: 20 residues within 4Å:- Chain H: T.33, N.35, A.40, R.41, R.70, N.95, K.99, D.152, Y.154, F.241, T.246, Y.248, E.250, Y.285
- Chain I: E.54, D.277, V.279, R.289
- Ligands: SAH.31, MG.33
22 PLIP interactions:17 interactions with chain H, 5 interactions with chain I- Hydrogen bonds: H:N.35, H:N.35, H:R.41, H:N.95, H:D.152, H:Y.248, H:Y.248, H:Y.285, I:D.277, I:V.279
- Water bridges: H:N.35, H:D.36, H:D.36, I:R.275, I:R.275
- Salt bridges: H:R.41, H:R.70, H:K.99, H:E.250
- pi-Stacking: H:Y.248, H:Y.248
- pi-Cation interactions: I:R.289
YG4.36: 19 residues within 4Å:- Chain I: T.33, N.35, A.40, R.41, R.70, N.95, K.99, D.152, Y.154, T.246, Y.248, E.250, Y.285
- Chain J: E.54, D.277, V.279, R.289
- Ligands: SAH.35, MG.37
21 PLIP interactions:15 interactions with chain I, 6 interactions with chain J- Hydrogen bonds: I:N.35, I:N.35, I:R.41, I:R.41, I:N.95, I:D.152, I:Y.248, I:Y.248, I:Y.285, J:D.277, J:V.279, J:R.289
- Salt bridges: I:R.41, I:R.70, I:K.99, I:E.250
- pi-Stacking: I:Y.248, I:Y.248
- Water bridges: J:R.275, J:R.275
- pi-Cation interactions: J:R.289
YG4.40: 18 residues within 4Å:- Chain J: N.35, A.40, R.41, R.70, K.99, D.152, Y.154, F.241, T.246, Y.248, E.250, Y.285
- Chain K: E.54, D.277, V.279, R.289
- Ligands: SAH.39, MG.41
18 PLIP interactions:14 interactions with chain J, 4 interactions with chain K- Hydrogen bonds: J:N.35, J:N.35, J:R.41, J:N.95, J:D.152, J:Y.248, J:Y.248, J:Y.285, K:D.277, K:V.279
- Salt bridges: J:R.41, J:R.70, J:K.99, J:E.250
- pi-Stacking: J:Y.248, J:Y.248
- Water bridges: K:R.275
- pi-Cation interactions: K:R.289
YG4.44: 20 residues within 4Å:- Chain K: T.33, N.35, A.40, R.41, R.70, N.95, K.99, D.152, Y.154, F.241, T.246, Y.248, E.250, Y.285
- Chain L: E.54, D.277, V.279, R.289
- Ligands: SAH.43, MG.45
22 PLIP interactions:5 interactions with chain L, 17 interactions with chain K- Hydrogen bonds: L:D.277, L:V.279, K:N.35, K:N.35, K:R.41, K:N.95, K:D.152, K:Y.248, K:Y.248, K:Y.285
- Water bridges: L:R.275, L:R.275, K:N.35, K:D.36, K:D.36
- pi-Cation interactions: L:R.289
- Salt bridges: K:R.41, K:R.70, K:K.99, K:E.250
- pi-Stacking: K:Y.248, K:Y.248
YG4.48: 19 residues within 4Å:- Chain A: E.54, D.277, V.279, R.289
- Chain L: T.33, N.35, A.40, R.41, R.70, N.95, K.99, D.152, Y.154, T.246, Y.248, E.250, Y.285
- Ligands: MG.4, SAH.47
21 PLIP interactions:15 interactions with chain L, 6 interactions with chain A- Hydrogen bonds: L:N.35, L:N.35, L:R.41, L:R.41, L:N.95, L:D.152, L:Y.248, L:Y.248, L:Y.285, A:D.277, A:V.279, A:R.289
- Salt bridges: L:R.41, L:R.70, L:K.99, L:E.250
- pi-Stacking: L:Y.248, L:Y.248
- Water bridges: A:R.275, A:R.275
- pi-Cation interactions: A:R.289
- 12 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
MG.4: 1 residues within 4Å:- Ligands: YG4.48
No protein-ligand interaction detected (PLIP)MG.5: 2 residues within 4Å:- Chain B: D.277
- Ligands: YG4.3
No protein-ligand interaction detected (PLIP)MG.9: 2 residues within 4Å:- Chain C: D.277
- Ligands: YG4.8
No protein-ligand interaction detected (PLIP)MG.13: 1 residues within 4Å:- Ligands: YG4.12
No protein-ligand interaction detected (PLIP)MG.17: 2 residues within 4Å:- Chain E: D.277
- Ligands: YG4.16
No protein-ligand interaction detected (PLIP)MG.21: 2 residues within 4Å:- Chain F: D.277
- Ligands: YG4.20
No protein-ligand interaction detected (PLIP)MG.25: 1 residues within 4Å:- Ligands: YG4.24
No protein-ligand interaction detected (PLIP)MG.29: 2 residues within 4Å:- Chain H: D.277
- Ligands: YG4.28
No protein-ligand interaction detected (PLIP)MG.33: 2 residues within 4Å:- Chain I: D.277
- Ligands: YG4.32
No protein-ligand interaction detected (PLIP)MG.37: 1 residues within 4Å:- Ligands: YG4.36
No protein-ligand interaction detected (PLIP)MG.41: 2 residues within 4Å:- Chain K: D.277
- Ligands: YG4.40
No protein-ligand interaction detected (PLIP)MG.45: 2 residues within 4Å:- Chain L: D.277
- Ligands: YG4.44
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Law, M.C.Y. et al., Chikungunya virus nonstructural protein 1 is a versatile RNA capping and decapping enzyme. J.Biol.Chem. (2023)
- Release Date
- 2023-11-15
- Peptides
- mRNA-capping enzyme nsP1: ABCDEFGHIJKL
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
GH
HI
IJ
JK
KL
L
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-12-mer
- Ligands
- 12 x ZN: ZINC ION(Non-covalent)
- 12 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)
- 12 x YG4: [(2~{R},3~{R},4~{R},5~{R})-5-(6-azanyl-7,8-dihydropurin-9-yl)-2-[[[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-4-methoxy-oxolan-3-yl] [(2~{R},3~{S},4~{R},5~{S})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate(Non-covalent)
- 12 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Law, M.C.Y. et al., Chikungunya virus nonstructural protein 1 is a versatile RNA capping and decapping enzyme. J.Biol.Chem. (2023)
- Release Date
- 2023-11-15
- Peptides
- mRNA-capping enzyme nsP1: ABCDEFGHIJKL
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
GH
HI
IJ
JK
KL
L