- 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: 12 residues within 4Å:- Chain A: G.65, R.70, P.83, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156
- Ligands: GTA.3
9 PLIP interactions:9 interactions with chain A- Hydrogen bonds: A:G.65, A:R.85, A:S.86, A:D.89, A:R.92, A:D.138, A:D.138, A:Q.151
- Salt bridges: A:R.70
SAH.8: 12 residues within 4Å:- Chain B: G.65, R.70, P.83, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156
- Ligands: GTA.9
9 PLIP interactions:9 interactions with chain B- Hydrogen bonds: B:G.65, B:R.85, B:S.86, B:D.89, B:R.92, B:D.138, B:D.138, B:Q.151
- Salt bridges: B:R.70
SAH.14: 12 residues within 4Å:- Chain C: G.65, R.70, P.83, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156
- Ligands: GTA.15
9 PLIP interactions:9 interactions with chain C- Hydrogen bonds: C:G.65, C:R.85, C:S.86, C:D.89, C:R.92, C:D.138, C:D.138, C:Q.151
- Salt bridges: C:R.70
SAH.20: 12 residues within 4Å:- Chain D: G.65, R.70, P.83, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156
- Ligands: GTA.21
9 PLIP interactions:9 interactions with chain D- Hydrogen bonds: D:G.65, D:R.85, D:S.86, D:D.89, D:R.92, D:D.138, D:D.138, D:Q.151
- Salt bridges: D:R.70
SAH.26: 12 residues within 4Å:- Chain E: G.65, R.70, P.83, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156
- Ligands: GTA.27
9 PLIP interactions:9 interactions with chain E- Hydrogen bonds: E:G.65, E:R.85, E:S.86, E:D.89, E:R.92, E:D.138, E:D.138, E:Q.151
- Salt bridges: E:R.70
SAH.32: 12 residues within 4Å:- Chain F: G.65, R.70, P.83, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156
- Ligands: GTA.33
9 PLIP interactions:9 interactions with chain F- Hydrogen bonds: F:G.65, F:R.85, F:S.86, F:D.89, F:R.92, F:D.138, F:D.138, F:Q.151
- Salt bridges: F:R.70
SAH.38: 12 residues within 4Å:- Chain G: G.65, R.70, P.83, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156
- Ligands: GTA.39
9 PLIP interactions:9 interactions with chain G- Hydrogen bonds: G:G.65, G:R.85, G:S.86, G:D.89, G:R.92, G:D.138, G:D.138, G:Q.151
- Salt bridges: G:R.70
SAH.44: 12 residues within 4Å:- Chain H: G.65, R.70, P.83, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156
- Ligands: GTA.45
9 PLIP interactions:9 interactions with chain H- Hydrogen bonds: H:G.65, H:R.85, H:S.86, H:D.89, H:R.92, H:D.138, H:D.138, H:Q.151
- Salt bridges: H:R.70
SAH.50: 12 residues within 4Å:- Chain I: G.65, R.70, P.83, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156
- Ligands: GTA.51
9 PLIP interactions:9 interactions with chain I- Hydrogen bonds: I:G.65, I:R.85, I:S.86, I:D.89, I:R.92, I:D.138, I:D.138, I:Q.151
- Salt bridges: I:R.70
SAH.56: 12 residues within 4Å:- Chain J: G.65, R.70, P.83, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156
- Ligands: GTA.57
9 PLIP interactions:9 interactions with chain J- Hydrogen bonds: J:G.65, J:R.85, J:S.86, J:D.89, J:R.92, J:D.138, J:D.138, J:Q.151
- Salt bridges: J:R.70
SAH.62: 12 residues within 4Å:- Chain K: G.65, R.70, P.83, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156
- Ligands: GTA.63
9 PLIP interactions:9 interactions with chain K- Hydrogen bonds: K:G.65, K:R.85, K:S.86, K:D.89, K:R.92, K:D.138, K:D.138, K:Q.151
- Salt bridges: K:R.70
SAH.68: 12 residues within 4Å:- Chain L: G.65, R.70, P.83, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156
- Ligands: GTA.69
9 PLIP interactions:9 interactions with chain L- Hydrogen bonds: L:G.65, L:R.85, L:S.86, L:D.89, L:R.92, L:D.138, L:D.138, L:Q.151
- Salt bridges: L:R.70
- 12 x GTA: P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE(Non-covalent)
GTA.3: 16 residues within 4Å:- Chain A: P.34, N.35, A.40, R.41, R.70, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285
- Chain B: V.279
- Ligands: SAH.2, U.4, MG.6
9 PLIP interactions:8 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:N.35, A:D.152, A:Y.248, A:Y.285, B:V.279
- Salt bridges: A:R.41, A:R.70, A:E.250
- pi-Stacking: A:Y.248
GTA.9: 16 residues within 4Å:- Chain B: P.34, N.35, A.40, R.41, R.70, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285
- Chain C: V.279
- Ligands: SAH.8, U.10, MG.12
9 PLIP interactions:8 interactions with chain B, 1 interactions with chain C- Hydrogen bonds: B:N.35, B:D.152, B:Y.248, B:Y.285, C:V.279
- Salt bridges: B:R.41, B:R.70, B:E.250
- pi-Stacking: B:Y.248
GTA.15: 16 residues within 4Å:- Chain C: P.34, N.35, A.40, R.41, R.70, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285
- Chain D: V.279
- Ligands: SAH.14, U.16, MG.18
9 PLIP interactions:8 interactions with chain C, 1 interactions with chain D- Hydrogen bonds: C:N.35, C:D.152, C:Y.248, C:Y.285, D:V.279
- Salt bridges: C:R.41, C:R.70, C:E.250
- pi-Stacking: C:Y.248
GTA.21: 16 residues within 4Å:- Chain D: P.34, N.35, A.40, R.41, R.70, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285
- Chain E: V.279
- Ligands: SAH.20, U.22, MG.24
9 PLIP interactions:8 interactions with chain D, 1 interactions with chain E- Hydrogen bonds: D:N.35, D:D.152, D:Y.248, D:Y.285, E:V.279
- Salt bridges: D:R.41, D:R.70, D:E.250
- pi-Stacking: D:Y.248
GTA.27: 16 residues within 4Å:- Chain E: P.34, N.35, A.40, R.41, R.70, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285
- Chain F: V.279
- Ligands: SAH.26, U.28, MG.30
9 PLIP interactions:1 interactions with chain F, 8 interactions with chain E- Hydrogen bonds: F:V.279, E:N.35, E:D.152, E:Y.248, E:Y.285
- Salt bridges: E:R.41, E:R.70, E:E.250
- pi-Stacking: E:Y.248
GTA.33: 16 residues within 4Å:- Chain F: P.34, N.35, A.40, R.41, R.70, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285
- Chain G: V.279
- Ligands: SAH.32, U.34, MG.36
9 PLIP interactions:8 interactions with chain F, 1 interactions with chain G- Hydrogen bonds: F:N.35, F:D.152, F:Y.248, F:Y.285, G:V.279
- Salt bridges: F:R.41, F:R.70, F:E.250
- pi-Stacking: F:Y.248
GTA.39: 16 residues within 4Å:- Chain G: P.34, N.35, A.40, R.41, R.70, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285
- Chain H: V.279
- Ligands: SAH.38, U.40, MG.42
9 PLIP interactions:8 interactions with chain G, 1 interactions with chain H- Hydrogen bonds: G:N.35, G:D.152, G:Y.248, G:Y.285, H:V.279
- Salt bridges: G:R.41, G:R.70, G:E.250
- pi-Stacking: G:Y.248
GTA.45: 16 residues within 4Å:- Chain H: P.34, N.35, A.40, R.41, R.70, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285
- Chain I: V.279
- Ligands: SAH.44, U.46, MG.48
9 PLIP interactions:8 interactions with chain H, 1 interactions with chain I- Hydrogen bonds: H:N.35, H:D.152, H:Y.248, H:Y.285, I:V.279
- Salt bridges: H:R.41, H:R.70, H:E.250
- pi-Stacking: H:Y.248
GTA.51: 16 residues within 4Å:- Chain I: P.34, N.35, A.40, R.41, R.70, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285
- Chain J: V.279
- Ligands: SAH.50, U.52, MG.54
9 PLIP interactions:8 interactions with chain I, 1 interactions with chain J- Hydrogen bonds: I:N.35, I:D.152, I:Y.248, I:Y.285, J:V.279
- Salt bridges: I:R.41, I:R.70, I:E.250
- pi-Stacking: I:Y.248
GTA.57: 16 residues within 4Å:- Chain J: P.34, N.35, A.40, R.41, R.70, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285
- Chain K: V.279
- Ligands: SAH.56, U.58, MG.60
9 PLIP interactions:1 interactions with chain K, 8 interactions with chain J- Hydrogen bonds: K:V.279, J:N.35, J:D.152, J:Y.248, J:Y.285
- Salt bridges: J:R.41, J:R.70, J:E.250
- pi-Stacking: J:Y.248
GTA.63: 16 residues within 4Å:- Chain K: P.34, N.35, A.40, R.41, R.70, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285
- Chain L: V.279
- Ligands: SAH.62, U.64, MG.66
9 PLIP interactions:8 interactions with chain K, 1 interactions with chain L- Hydrogen bonds: K:N.35, K:D.152, K:Y.248, K:Y.285, L:V.279
- Salt bridges: K:R.41, K:R.70, K:E.250
- pi-Stacking: K:Y.248
GTA.69: 16 residues within 4Å:- Chain A: V.279
- Chain L: P.34, N.35, A.40, R.41, R.70, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285
- Ligands: SAH.68, U.70, MG.72
9 PLIP interactions:8 interactions with chain L, 1 interactions with chain A- Hydrogen bonds: L:N.35, L:D.152, L:Y.248, L:Y.285, A:V.279
- Salt bridges: L:R.41, L:R.70, L:E.250
- pi-Stacking: L:Y.248
- 12 x U: URIDINE-5'-MONOPHOSPHATE(Non-covalent)
U.4: 8 residues within 4Å:- Chain A: Y.5, V.6, D.7, R.41, A.42, H.45
- Ligands: GTA.3, G.5
8 PLIP interactions:4 interactions with chain B, 4 interactions with chain A- Hydrophobic interactions: B:R.41, A:R.41
- Hydrogen bonds: B:Y.5, B:D.7, A:Y.5, A:D.7
- pi-Stacking: B:H.45, A:H.45
U.10: 8 residues within 4Å:- Chain B: Y.5, V.6, D.7, R.41, A.42, H.45
- Ligands: GTA.9, G.11
Protein-ligand interaction information (PLIP) not availableU.16: 8 residues within 4Å:- Chain C: Y.5, V.6, D.7, R.41, A.42, H.45
- Ligands: GTA.15, G.17
12 PLIP interactions:4 interactions with chain C, 4 interactions with chain D, 4 interactions with chain E- Hydrophobic interactions: C:R.41, D:R.41, E:R.41
- Hydrogen bonds: C:Y.5, C:D.7, D:Y.5, D:D.7, E:Y.5, E:D.7
- pi-Stacking: C:H.45, D:H.45, E:H.45
U.22: 8 residues within 4Å:- Chain D: Y.5, V.6, D.7, R.41, A.42, H.45
- Ligands: GTA.21, G.23
Protein-ligand interaction information (PLIP) not availableU.28: 8 residues within 4Å:- Chain E: Y.5, V.6, D.7, R.41, A.42, H.45
- Ligands: GTA.27, G.29
Protein-ligand interaction information (PLIP) not availableU.34: 8 residues within 4Å:- Chain F: Y.5, V.6, D.7, R.41, A.42, H.45
- Ligands: GTA.33, G.35
8 PLIP interactions:4 interactions with chain G, 4 interactions with chain F- Hydrophobic interactions: G:R.41, F:R.41
- Hydrogen bonds: G:Y.5, G:D.7, F:Y.5, F:D.7
- pi-Stacking: G:H.45, F:H.45
U.40: 8 residues within 4Å:- Chain G: Y.5, V.6, D.7, R.41, A.42, H.45
- Ligands: GTA.39, G.41
Protein-ligand interaction information (PLIP) not availableU.46: 8 residues within 4Å:- Chain H: Y.5, V.6, D.7, R.41, A.42, H.45
- Ligands: GTA.45, G.47
12 PLIP interactions:4 interactions with chain J, 4 interactions with chain I, 4 interactions with chain H- Hydrophobic interactions: J:R.41, I:R.41, H:R.41
- Hydrogen bonds: J:Y.5, J:D.7, I:Y.5, I:D.7, H:Y.5, H:D.7
- pi-Stacking: J:H.45, I:H.45, H:H.45
U.52: 8 residues within 4Å:- Chain I: Y.5, V.6, D.7, R.41, A.42, H.45
- Ligands: GTA.51, G.53
Protein-ligand interaction information (PLIP) not availableU.58: 8 residues within 4Å:- Chain J: Y.5, V.6, D.7, R.41, A.42, H.45
- Ligands: GTA.57, G.59
Protein-ligand interaction information (PLIP) not availableU.64: 8 residues within 4Å:- Chain K: Y.5, V.6, D.7, R.41, A.42, H.45
- Ligands: GTA.63, G.65
8 PLIP interactions:4 interactions with chain L, 4 interactions with chain K- Hydrophobic interactions: L:R.41, K:R.41
- Hydrogen bonds: L:Y.5, L:D.7, K:Y.5, K:D.7
- pi-Stacking: L:H.45, K:H.45
U.70: 8 residues within 4Å:- Chain L: Y.5, V.6, D.7, R.41, A.42, H.45
- Ligands: GTA.69, G.71
Protein-ligand interaction information (PLIP) not available- 12 x G: GUANOSINE-5'-MONOPHOSPHATE(Non-functional Binders)
G.5: 1 residues within 4Å:- Ligands: U.4
Protein-ligand interaction information (PLIP) not availableG.11: 1 residues within 4Å:- Ligands: U.10
Protein-ligand interaction information (PLIP) not availableG.17: 1 residues within 4Å:- Ligands: U.16
Protein-ligand interaction information (PLIP) not availableG.23: 1 residues within 4Å:- Ligands: U.22
Protein-ligand interaction information (PLIP) not availableG.29: 1 residues within 4Å:- Ligands: U.28
Protein-ligand interaction information (PLIP) not availableG.35: 1 residues within 4Å:- Ligands: U.34
Protein-ligand interaction information (PLIP) not availableG.41: 1 residues within 4Å:- Ligands: U.40
Protein-ligand interaction information (PLIP) not availableG.47: 1 residues within 4Å:- Ligands: U.46
Protein-ligand interaction information (PLIP) not availableG.53: 1 residues within 4Å:- Ligands: U.52
Protein-ligand interaction information (PLIP) not availableG.59: 1 residues within 4Å:- Ligands: U.58
Protein-ligand interaction information (PLIP) not availableG.65: 1 residues within 4Å:- Ligands: U.64
Protein-ligand interaction information (PLIP) not availableG.71: 1 residues within 4Å:- Ligands: U.70
Protein-ligand interaction information (PLIP) not available- 12 x MG: MAGNESIUM ION(Non-functional Binders)
MG.6: 1 residues within 4Å:- Ligands: GTA.3
No protein-ligand interaction detected (PLIP)MG.12: 1 residues within 4Å:- Ligands: GTA.9
No protein-ligand interaction detected (PLIP)MG.18: 1 residues within 4Å:- Ligands: GTA.15
No protein-ligand interaction detected (PLIP)MG.24: 1 residues within 4Å:- Ligands: GTA.21
No protein-ligand interaction detected (PLIP)MG.30: 1 residues within 4Å:- Ligands: GTA.27
No protein-ligand interaction detected (PLIP)MG.36: 1 residues within 4Å:- Ligands: GTA.33
No protein-ligand interaction detected (PLIP)MG.42: 1 residues within 4Å:- Ligands: GTA.39
No protein-ligand interaction detected (PLIP)MG.48: 1 residues within 4Å:- Ligands: GTA.45
No protein-ligand interaction detected (PLIP)MG.54: 1 residues within 4Å:- Ligands: GTA.51
No protein-ligand interaction detected (PLIP)MG.60: 1 residues within 4Å:- Ligands: GTA.57
No protein-ligand interaction detected (PLIP)MG.66: 1 residues within 4Å:- Ligands: GTA.63
No protein-ligand interaction detected (PLIP)MG.72: 1 residues within 4Å:- Ligands: GTA.69
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zhang, K. et al., Molecular basis of specific viral RNA recognition and 5'-end capping by the Chikungunya virus nsP1. Cell Rep (2022)
- Release Date
- 2022-07-27
- 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 GTA: P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE(Non-covalent)
- 12 x U: URIDINE-5'-MONOPHOSPHATE(Non-covalent)
- 12 x G: GUANOSINE-5'-MONOPHOSPHATE(Non-functional Binders)
- 12 x MG: MAGNESIUM ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zhang, K. et al., Molecular basis of specific viral RNA recognition and 5'-end capping by the Chikungunya virus nsP1. Cell Rep (2022)
- Release Date
- 2022-07-27
- 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