- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.80 Å
- Oligo State
- homo-12-mer
- Ligands
- 24 x MG: MAGNESIUM ION(Non-covalent)
- 12 x NA: SODIUM ION(Non-functional Binders)
NA.3: 5 residues within 4Å:- Ligands: CL.5, NA.21, CL.23, NA.27, CL.29
No protein-ligand interaction detected (PLIP)NA.9: 5 residues within 4Å:- Ligands: CL.11, NA.45, CL.47, NA.57, CL.59
No protein-ligand interaction detected (PLIP)NA.15: 5 residues within 4Å:- Ligands: CL.17, NA.39, CL.41, NA.63, CL.65
No protein-ligand interaction detected (PLIP)NA.21: 5 residues within 4Å:- Ligands: NA.3, CL.5, CL.23, NA.27, CL.29
No protein-ligand interaction detected (PLIP)NA.27: 5 residues within 4Å:- Ligands: NA.3, CL.5, NA.21, CL.23, CL.29
No protein-ligand interaction detected (PLIP)NA.33: 5 residues within 4Å:- Ligands: CL.35, NA.51, CL.53, NA.69, CL.71
No protein-ligand interaction detected (PLIP)NA.39: 5 residues within 4Å:- Ligands: NA.15, CL.17, CL.41, NA.63, CL.65
No protein-ligand interaction detected (PLIP)NA.45: 5 residues within 4Å:- Ligands: NA.9, CL.11, CL.47, NA.57, CL.59
No protein-ligand interaction detected (PLIP)NA.51: 5 residues within 4Å:- Ligands: NA.33, CL.35, CL.53, NA.69, CL.71
No protein-ligand interaction detected (PLIP)NA.57: 5 residues within 4Å:- Ligands: NA.9, CL.11, NA.45, CL.47, CL.59
No protein-ligand interaction detected (PLIP)NA.63: 5 residues within 4Å:- Ligands: NA.15, CL.17, NA.39, CL.41, CL.65
No protein-ligand interaction detected (PLIP)NA.69: 5 residues within 4Å:- Ligands: NA.33, CL.35, NA.51, CL.53, CL.71
No protein-ligand interaction detected (PLIP)- 12 x CF4: [4-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)butyl]carbamic acid
CF4.4: 10 residues within 4Å:- Chain A: F.2, V.34, W.35, A.36
- Chain B: V.43, A.44, I.45, Q.52
- Chain D: Q.52
- Ligands: CF4.46
11 PLIP interactions:1 interactions with chain B, 8 interactions with chain A, 2 interactions with chain D- Water bridges: B:G.46, A:K.4, A:K.4
- Hydrophobic interactions: A:W.35, A:W.35
- pi-Stacking: A:W.35, A:W.35, A:W.35, A:W.35
- Hydrogen bonds: D:Q.52, D:Q.52
CF4.10: 10 residues within 4Å:- Chain B: F.2, V.34, W.35, A.36
- Chain C: V.43, A.44, I.45, Q.52
- Chain J: Q.52
- Ligands: CF4.64
11 PLIP interactions:8 interactions with chain B, 1 interactions with chain C, 2 interactions with chain J- Hydrophobic interactions: B:W.35, B:W.35
- Water bridges: B:K.4, B:K.4, C:G.46
- pi-Stacking: B:W.35, B:W.35, B:W.35, B:W.35
- Hydrogen bonds: J:Q.52, J:Q.52
CF4.16: 10 residues within 4Å:- Chain A: V.43, A.44, I.45, Q.52
- Chain C: F.2, V.34, W.35, A.36
- Chain G: Q.52
- Ligands: CF4.28
11 PLIP interactions:1 interactions with chain A, 8 interactions with chain C, 2 interactions with chain G- Water bridges: A:G.46, C:K.4, C:K.4
- Hydrophobic interactions: C:W.35, C:W.35
- pi-Stacking: C:W.35, C:W.35, C:W.35, C:W.35
- Hydrogen bonds: G:Q.52, G:Q.52
CF4.22: 10 residues within 4Å:- Chain D: F.2, V.34, W.35, A.36
- Chain E: Q.52
- Chain F: V.43, A.44, I.45, Q.52
- Ligands: CF4.52
11 PLIP interactions:8 interactions with chain D, 1 interactions with chain F, 2 interactions with chain E- Hydrophobic interactions: D:W.35, D:W.35
- Water bridges: D:K.4, D:K.4, F:G.46
- pi-Stacking: D:W.35, D:W.35, D:W.35, D:W.35
- Hydrogen bonds: E:Q.52, E:Q.52
CF4.28: 10 residues within 4Å:- Chain A: Q.52
- Chain E: F.2, V.34, W.35, A.36
- Chain G: V.43, A.44, I.45, Q.52
- Ligands: CF4.16
11 PLIP interactions:8 interactions with chain E, 2 interactions with chain A, 1 interactions with chain G- Hydrophobic interactions: E:W.35, E:W.35
- Water bridges: E:K.4, E:K.4, G:G.46
- pi-Stacking: E:W.35, E:W.35, E:W.35, E:W.35
- Hydrogen bonds: A:Q.52, A:Q.52
CF4.34: 10 residues within 4Å:- Chain F: F.2, V.34, W.35, A.36
- Chain H: V.43, A.44, I.45, Q.52
- Chain L: Q.52
- Ligands: CF4.58
11 PLIP interactions:8 interactions with chain F, 1 interactions with chain H, 2 interactions with chain L- Hydrophobic interactions: F:W.35, F:W.35
- Water bridges: F:K.4, F:K.4, H:G.46
- pi-Stacking: F:W.35, F:W.35, F:W.35, F:W.35
- Hydrogen bonds: L:Q.52, L:Q.52
CF4.40: 10 residues within 4Å:- Chain G: F.2, V.34, W.35, A.36
- Chain I: V.43, A.44, I.45, Q.52
- Chain K: Q.52
- Ligands: CF4.70
11 PLIP interactions:1 interactions with chain I, 8 interactions with chain G, 2 interactions with chain K- Water bridges: I:G.46, G:K.4, G:K.4
- Hydrophobic interactions: G:W.35, G:W.35
- pi-Stacking: G:W.35, G:W.35, G:W.35, G:W.35
- Hydrogen bonds: K:Q.52, K:Q.52
CF4.46: 10 residues within 4Å:- Chain B: Q.52
- Chain D: V.43, A.44, I.45, Q.52
- Chain H: F.2, V.34, W.35, A.36
- Ligands: CF4.4
11 PLIP interactions:2 interactions with chain B, 8 interactions with chain H, 1 interactions with chain D- Hydrogen bonds: B:Q.52, B:Q.52
- Hydrophobic interactions: H:W.35, H:W.35
- Water bridges: H:K.4, H:K.4, D:G.46
- pi-Stacking: H:W.35, H:W.35, H:W.35, H:W.35
CF4.52: 10 residues within 4Å:- Chain E: V.43, A.44, I.45, Q.52
- Chain F: Q.52
- Chain I: F.2, V.34, W.35, A.36
- Ligands: CF4.22
11 PLIP interactions:8 interactions with chain I, 1 interactions with chain E, 2 interactions with chain F- Hydrophobic interactions: I:W.35, I:W.35
- Water bridges: I:K.4, I:K.4, E:G.46
- pi-Stacking: I:W.35, I:W.35, I:W.35, I:W.35
- Hydrogen bonds: F:Q.52, F:Q.52
CF4.58: 10 residues within 4Å:- Chain H: Q.52
- Chain J: F.2, V.34, W.35, A.36
- Chain L: V.43, A.44, I.45, Q.52
- Ligands: CF4.34
11 PLIP interactions:1 interactions with chain L, 8 interactions with chain J, 2 interactions with chain H- Water bridges: L:G.46, J:K.4, J:K.4
- Hydrophobic interactions: J:W.35, J:W.35
- pi-Stacking: J:W.35, J:W.35, J:W.35, J:W.35
- Hydrogen bonds: H:Q.52, H:Q.52
CF4.64: 10 residues within 4Å:- Chain C: Q.52
- Chain J: V.43, A.44, I.45, Q.52
- Chain K: F.2, V.34, W.35, A.36
- Ligands: CF4.10
11 PLIP interactions:1 interactions with chain J, 8 interactions with chain K, 2 interactions with chain C- Water bridges: J:G.46, K:K.4, K:K.4
- Hydrophobic interactions: K:W.35, K:W.35
- pi-Stacking: K:W.35, K:W.35, K:W.35, K:W.35
- Hydrogen bonds: C:Q.52, C:Q.52
CF4.70: 10 residues within 4Å:- Chain I: Q.52
- Chain K: V.43, A.44, I.45, Q.52
- Chain L: F.2, V.34, W.35, A.36
- Ligands: CF4.40
11 PLIP interactions:1 interactions with chain K, 8 interactions with chain L, 2 interactions with chain I- Water bridges: K:G.46, L:K.4, L:K.4
- Hydrophobic interactions: L:W.35, L:W.35
- pi-Stacking: L:W.35, L:W.35, L:W.35, L:W.35
- Hydrogen bonds: I:Q.52, I:Q.52
- 12 x CL: CHLORIDE ION(Non-functional Binders)
CL.5: 8 residues within 4Å:- Chain A: Q.56
- Chain D: Q.56
- Chain E: Q.56
- Ligands: NA.3, NA.21, CL.23, NA.27, CL.29
Ligand excluded by PLIPCL.11: 8 residues within 4Å:- Chain B: Q.56
- Chain H: Q.56
- Chain J: Q.56
- Ligands: NA.9, NA.45, CL.47, NA.57, CL.59
Ligand excluded by PLIPCL.17: 8 residues within 4Å:- Chain C: Q.56
- Chain G: Q.56
- Chain K: Q.56
- Ligands: NA.15, NA.39, CL.41, NA.63, CL.65
Ligand excluded by PLIPCL.23: 8 residues within 4Å:- Chain A: Q.56
- Chain D: Q.56
- Chain E: Q.56
- Ligands: NA.3, CL.5, NA.21, NA.27, CL.29
Ligand excluded by PLIPCL.29: 8 residues within 4Å:- Chain A: Q.56
- Chain D: Q.56
- Chain E: Q.56
- Ligands: NA.3, CL.5, NA.21, CL.23, NA.27
Ligand excluded by PLIPCL.35: 8 residues within 4Å:- Chain F: Q.56
- Chain I: Q.56
- Chain L: Q.56
- Ligands: NA.33, NA.51, CL.53, NA.69, CL.71
Ligand excluded by PLIPCL.41: 8 residues within 4Å:- Chain C: Q.56
- Chain G: Q.56
- Chain K: Q.56
- Ligands: NA.15, CL.17, NA.39, NA.63, CL.65
Ligand excluded by PLIPCL.47: 8 residues within 4Å:- Chain B: Q.56
- Chain H: Q.56
- Chain J: Q.56
- Ligands: NA.9, CL.11, NA.45, NA.57, CL.59
Ligand excluded by PLIPCL.53: 8 residues within 4Å:- Chain F: Q.56
- Chain I: Q.56
- Chain L: Q.56
- Ligands: NA.33, CL.35, NA.51, NA.69, CL.71
Ligand excluded by PLIPCL.59: 8 residues within 4Å:- Chain B: Q.56
- Chain H: Q.56
- Chain J: Q.56
- Ligands: NA.9, CL.11, NA.45, CL.47, NA.57
Ligand excluded by PLIPCL.65: 8 residues within 4Å:- Chain C: Q.56
- Chain G: Q.56
- Chain K: Q.56
- Ligands: NA.15, CL.17, NA.39, CL.41, NA.63
Ligand excluded by PLIPCL.71: 8 residues within 4Å:- Chain F: Q.56
- Chain I: Q.56
- Chain L: Q.56
- Ligands: NA.33, CL.35, NA.51, CL.53, NA.69
Ligand excluded by PLIP- 12 x SO4: SULFATE ION(Non-functional Binders)
SO4.6: 11 residues within 4Å:- Chain A: S.14, F.15, T.16
- Chain B: S.14, F.15, T.16
- Chain C: S.14, F.15, T.16
- Ligands: SO4.12, SO4.18
10 PLIP interactions:4 interactions with chain A, 4 interactions with chain C, 2 interactions with chain B- Hydrogen bonds: A:F.15, A:T.16, A:T.16, A:T.16, C:F.15, C:T.16, C:T.16, C:T.16, B:T.16, B:T.16
SO4.12: 11 residues within 4Å:- Chain A: S.14, F.15, T.16
- Chain B: S.14, F.15, T.16
- Chain C: S.14, F.15, T.16
- Ligands: SO4.6, SO4.18
10 PLIP interactions:4 interactions with chain A, 2 interactions with chain C, 4 interactions with chain B- Hydrogen bonds: A:F.15, A:T.16, A:T.16, A:T.16, C:T.16, C:T.16, B:F.15, B:T.16, B:T.16, B:T.16
SO4.18: 11 residues within 4Å:- Chain A: S.14, F.15, T.16
- Chain B: S.14, F.15, T.16
- Chain C: S.14, F.15, T.16
- Ligands: SO4.6, SO4.12
10 PLIP interactions:4 interactions with chain C, 4 interactions with chain B, 2 interactions with chain A- Hydrogen bonds: C:F.15, C:T.16, C:T.16, C:T.16, B:F.15, B:T.16, B:T.16, B:T.16, A:T.16, A:T.16
SO4.24: 11 residues within 4Å:- Chain D: S.14, F.15, T.16
- Chain F: S.14, F.15, T.16
- Chain H: S.14, F.15, T.16
- Ligands: SO4.36, SO4.48
10 PLIP interactions:4 interactions with chain D, 2 interactions with chain F, 4 interactions with chain H- Hydrogen bonds: D:F.15, D:T.16, D:T.16, D:T.16, F:T.16, F:T.16, H:F.15, H:T.16, H:T.16, H:T.16
SO4.30: 11 residues within 4Å:- Chain E: S.14, F.15, T.16
- Chain G: S.14, F.15, T.16
- Chain I: S.14, F.15, T.16
- Ligands: SO4.42, SO4.54
10 PLIP interactions:4 interactions with chain I, 4 interactions with chain E, 2 interactions with chain G- Hydrogen bonds: I:F.15, I:T.16, I:T.16, I:T.16, E:F.15, E:T.16, E:T.16, E:T.16, G:T.16, G:T.16
SO4.36: 11 residues within 4Å:- Chain D: S.14, F.15, T.16
- Chain F: S.14, F.15, T.16
- Chain H: S.14, F.15, T.16
- Ligands: SO4.24, SO4.48
10 PLIP interactions:4 interactions with chain D, 2 interactions with chain H, 4 interactions with chain F- Hydrogen bonds: D:F.15, D:T.16, D:T.16, D:T.16, H:T.16, H:T.16, F:F.15, F:T.16, F:T.16, F:T.16
SO4.42: 11 residues within 4Å:- Chain E: S.14, F.15, T.16
- Chain G: S.14, F.15, T.16
- Chain I: S.14, F.15, T.16
- Ligands: SO4.30, SO4.54
10 PLIP interactions:4 interactions with chain G, 4 interactions with chain E, 2 interactions with chain I- Hydrogen bonds: G:F.15, G:T.16, G:T.16, G:T.16, E:F.15, E:T.16, E:T.16, E:T.16, I:T.16, I:T.16
SO4.48: 11 residues within 4Å:- Chain D: S.14, F.15, T.16
- Chain F: S.14, F.15, T.16
- Chain H: S.14, F.15, T.16
- Ligands: SO4.24, SO4.36
10 PLIP interactions:2 interactions with chain D, 4 interactions with chain F, 4 interactions with chain H- Hydrogen bonds: D:T.16, D:T.16, F:F.15, F:T.16, F:T.16, F:T.16, H:F.15, H:T.16, H:T.16, H:T.16
SO4.54: 11 residues within 4Å:- Chain E: S.14, F.15, T.16
- Chain G: S.14, F.15, T.16
- Chain I: S.14, F.15, T.16
- Ligands: SO4.30, SO4.42
10 PLIP interactions:4 interactions with chain I, 2 interactions with chain E, 4 interactions with chain G- Hydrogen bonds: I:F.15, I:T.16, I:T.16, I:T.16, E:T.16, E:T.16, G:F.15, G:T.16, G:T.16, G:T.16
SO4.60: 11 residues within 4Å:- Chain J: S.14, F.15, T.16
- Chain K: S.14, F.15, T.16
- Chain L: S.14, F.15, T.16
- Ligands: SO4.66, SO4.72
10 PLIP interactions:2 interactions with chain L, 4 interactions with chain J, 4 interactions with chain K- Hydrogen bonds: L:T.16, L:T.16, J:F.15, J:T.16, J:T.16, J:T.16, K:F.15, K:T.16, K:T.16, K:T.16
SO4.66: 11 residues within 4Å:- Chain J: S.14, F.15, T.16
- Chain K: S.14, F.15, T.16
- Chain L: S.14, F.15, T.16
- Ligands: SO4.60, SO4.72
10 PLIP interactions:4 interactions with chain K, 4 interactions with chain L, 2 interactions with chain J- Hydrogen bonds: K:F.15, K:T.16, K:T.16, K:T.16, L:F.15, L:T.16, L:T.16, L:T.16, J:T.16, J:T.16
SO4.72: 11 residues within 4Å:- Chain J: S.14, F.15, T.16
- Chain K: S.14, F.15, T.16
- Chain L: S.14, F.15, T.16
- Ligands: SO4.60, SO4.66
10 PLIP interactions:4 interactions with chain J, 2 interactions with chain K, 4 interactions with chain L- Hydrogen bonds: J:F.15, J:T.16, J:T.16, J:T.16, K:T.16, K:T.16, L:F.15, L:T.16, L:T.16, L:T.16
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Grininger, M. et al., Electrochemical Switching of the Flavoprotein Dodecin at Gold Surfaces Modified by Flavin-DNA Hybrid Linkers. Biointerphases (2008)
- Release Date
- 2008-09-30
- Peptides
- DODECIN: ABCDEFGHIJKL
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
AE
AF
AG
AH
AI
AJ
AK
AL
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.80 Å
- Oligo State
- homo-12-mer
- Ligands
- 24 x MG: MAGNESIUM ION(Non-covalent)
- 12 x NA: SODIUM ION(Non-functional Binders)
- 12 x CF4: [4-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)butyl]carbamic acid
- 12 x CL: CHLORIDE ION(Non-functional Binders)
- 12 x SO4: SULFATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Grininger, M. et al., Electrochemical Switching of the Flavoprotein Dodecin at Gold Surfaces Modified by Flavin-DNA Hybrid Linkers. Biointerphases (2008)
- Release Date
- 2008-09-30
- Peptides
- DODECIN: ABCDEFGHIJKL
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
AE
AF
AG
AH
AI
AJ
AK
AL
A