SMTL ID : 1mog.1

Crystal structure of H. salinarum dodecin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-12-mer

Ligands

24 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: E.13, E.50 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.13, H2O.1, H2O.1, H2O.1, H2O.2, H2O.2 MG.2: 1 residues within 4Å: Chain K: D.40 6 PLIP interactions: 1 interactions with chain K, 5 Ligand-Water interactions Metal complexes: K:D.40, H2O.3, H2O.4, H2O.4, H2O.4, H2O.41 MG.7: 2 residues within 4Å: Chain B: E.13, E.50 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:E.13, H2O.4, H2O.4, H2O.5, H2O.6, H2O.6 MG.8: 1 residues within 4Å: Chain F: D.40 6 PLIP interactions: 1 interactions with chain F, 5 Ligand-Water interactions Metal complexes: F:D.40, H2O.7, H2O.7, H2O.7, H2O.8, H2O.23 MG.13: 2 residues within 4Å: Chain C: E.13, E.50 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:E.13, H2O.8, H2O.8, H2O.9, H2O.9, H2O.9 MG.14: 1 residues within 4Å: Chain G: D.40 6 PLIP interactions: 1 interactions with chain G, 5 Ligand-Water interactions Metal complexes: G:D.40, H2O.11, H2O.11, H2O.11, H2O.12, H2O.26 MG.19: 2 residues within 4Å: Chain D: E.13, E.50 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:E.13, H2O.12, H2O.12, H2O.13, H2O.13, H2O.13 MG.20: 1 residues within 4Å: Chain H: D.40 6 PLIP interactions: 1 interactions with chain H, 5 Ligand-Water interactions Metal complexes: H:D.40, H2O.14, H2O.15, H2O.15, H2O.15, H2O.30 MG.25: 2 residues within 4Å: Chain E: E.13, E.50 6 PLIP interactions: 1 interactions with chain E, 5 Ligand-Water interactions Metal complexes: E:E.13, H2O.16, H2O.16, H2O.17, H2O.17, H2O.17 MG.26: 1 residues within 4Å: Chain C: D.40 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:D.40, H2O.11, H2O.18, H2O.19, H2O.19, H2O.19 MG.31: 2 residues within 4Å: Chain F: E.13, E.50 6 PLIP interactions: 1 interactions with chain F, 5 Ligand-Water interactions Metal complexes: F:E.13, H2O.19, H2O.19, H2O.20, H2O.21, H2O.21 MG.32: 1 residues within 4Å: Chain J: D.40 6 PLIP interactions: 1 interactions with chain J, 5 Ligand-Water interactions Metal complexes: J:D.40, H2O.22, H2O.22, H2O.22, H2O.23, H2O.38 MG.37: 2 residues within 4Å: Chain G: E.13, E.50 6 PLIP interactions: 1 interactions with chain G, 5 Ligand-Water interactions Metal complexes: G:E.13, H2O.23, H2O.23, H2O.24, H2O.24, H2O.25 MG.38: 1 residues within 4Å: Chain E: D.40 6 PLIP interactions: 1 interactions with chain E, 5 Ligand-Water interactions Metal complexes: E:D.40, H2O.19, H2O.26, H2O.26, H2O.26, H2O.27 MG.43: 2 residues within 4Å: Chain H: E.13, E.50 6 PLIP interactions: 1 interactions with chain H, 5 Ligand-Water interactions Metal complexes: H:E.13, H2O.27, H2O.27, H2O.28, H2O.28, H2O.28 MG.44: 1 residues within 4Å: Chain L: D.40 6 PLIP interactions: 1 interactions with chain L, 5 Ligand-Water interactions Metal complexes: L:D.40, H2O.29, H2O.30, H2O.30, H2O.30, H2O.45 MG.49: 2 residues within 4Å: Chain I: E.13, E.50 6 PLIP interactions: 1 interactions with chain I, 5 Ligand-Water interactions Metal complexes: I:E.13, H2O.31, H2O.31, H2O.32, H2O.32, H2O.32 MG.50: 1 residues within 4Å: Chain A: D.40 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.40, H2O.4, H2O.33, H2O.34, H2O.34, H2O.34 MG.55: 2 residues within 4Å: Chain J: E.13, E.50 6 PLIP interactions: 1 interactions with chain J, 5 Ligand-Water interactions Metal complexes: J:E.13, H2O.34, H2O.35, H2O.35, H2O.36, H2O.36 MG.56: 1 residues within 4Å: Chain B: D.40 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.40, H2O.7, H2O.37, H2O.37, H2O.38, H2O.38 MG.61: 2 residues within 4Å: Chain K: E.13, E.50 6 PLIP interactions: 1 interactions with chain K, 5 Ligand-Water interactions Metal complexes: K:E.13, H2O.38, H2O.38, H2O.39, H2O.39, H2O.40 MG.62: 1 residues within 4Å: Chain I: D.40 6 PLIP interactions: 1 interactions with chain I, 5 Ligand-Water interactions Metal complexes: I:D.40, H2O.34, H2O.41, H2O.41, H2O.41, H2O.42 MG.67: 2 residues within 4Å: Chain L: E.13, E.50 6 PLIP interactions: 1 interactions with chain L, 5 Ligand-Water interactions Metal complexes: L:E.13, H2O.42, H2O.42, H2O.43, H2O.43, H2O.43 MG.68: 1 residues within 4Å: Chain D: D.40 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:D.40, H2O.15, H2O.45, H2O.45, H2O.45, H2O.45

12 x NA: SODIUM ION(Non-functional Binders)

NA.3: 5 residues within 4Å: Ligands: CL.4, NA.51, CL.52, NA.63, CL.64 6 PLIP interactions: 2 interactions with chain K, 2 interactions with chain A, 2 interactions with chain I Water bridges: K:K.4, K:L.6, A:K.4, A:L.6, I:K.4, I:L.6 NA.9: 5 residues within 4Å: Ligands: CL.10, NA.33, CL.34, NA.57, CL.58 4 PLIP interactions: 1 interactions with chain F, 2 interactions with chain B, 1 interactions with chain J Water bridges: F:L.6, B:K.4, B:L.6, J:L.6 NA.15: 5 residues within 4Å: Ligands: CL.16, NA.27, CL.28, NA.39, CL.40 6 PLIP interactions: 2 interactions with chain G, 2 interactions with chain E, 2 interactions with chain C Water bridges: G:K.4, G:L.6, E:K.4, E:L.6, C:K.4, C:L.6 NA.21: 5 residues within 4Å: Ligands: CL.22, NA.45, CL.46, NA.69, CL.70 6 PLIP interactions: 2 interactions with chain L, 2 interactions with chain D, 2 interactions with chain H Water bridges: L:K.4, L:L.6, D:K.4, D:L.6, H:K.4, H:L.6 NA.27: 5 residues within 4Å: Ligands: NA.15, CL.16, CL.28, NA.39, CL.40 5 PLIP interactions: 1 interactions with chain G, 2 interactions with chain C, 2 interactions with chain E Water bridges: G:L.6, C:K.4, C:L.6, E:K.4, E:L.6 NA.33: 5 residues within 4Å: Ligands: NA.9, CL.10, CL.34, NA.57, CL.58 4 PLIP interactions: 1 interactions with chain F, 2 interactions with chain B, 1 interactions with chain J Water bridges: F:L.6, B:K.4, B:L.6, J:L.6 NA.39: 5 residues within 4Å: Ligands: NA.15, CL.16, NA.27, CL.28, CL.40 6 PLIP interactions: 2 interactions with chain G, 2 interactions with chain C, 2 interactions with chain E Water bridges: G:K.4, G:L.6, C:K.4, C:L.6, E:K.4, E:L.6 NA.45: 5 residues within 4Å: Ligands: NA.21, CL.22, CL.46, NA.69, CL.70 4 PLIP interactions: 1 interactions with chain H, 2 interactions with chain L, 1 interactions with chain D Water bridges: H:L.6, L:K.4, L:L.6, D:L.6 NA.51: 5 residues within 4Å: Ligands: NA.3, CL.4, CL.52, NA.63, CL.64 5 PLIP interactions: 2 interactions with chain I, 2 interactions with chain K, 1 interactions with chain A Water bridges: I:K.4, I:L.6, K:K.4, K:L.6, A:L.6 NA.57: 5 residues within 4Å: Ligands: NA.9, CL.10, NA.33, CL.34, CL.58 6 PLIP interactions: 2 interactions with chain F, 2 interactions with chain B, 2 interactions with chain J Water bridges: F:K.4, F:L.6, B:K.4, B:L.6, J:K.4, J:L.6 NA.63: 5 residues within 4Å: Ligands: NA.3, CL.4, NA.51, CL.52, CL.64 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain I, 2 interactions with chain K Water bridges: A:K.4, A:L.6, I:K.4, I:L.6, K:K.4, K:L.6 NA.69: 5 residues within 4Å: Ligands: NA.21, CL.22, NA.45, CL.46, CL.70 6 PLIP interactions: 2 interactions with chain D, 2 interactions with chain L, 2 interactions with chain H Water bridges: D:K.4, D:L.6, L:K.4, L:L.6, H:K.4, H:L.6

24 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 8 residues within 4Å: Chain A: Q.58 Chain I: Q.58 Chain K: Q.58 Ligands: NA.3, NA.51, CL.52, NA.63, CL.64 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: T.16 Chain B: T.16 Chain C: T.16 Ligands: CL.11, CL.17 Ligand excluded by PLIP CL.10: 8 residues within 4Å: Chain B: Q.58 Chain F: Q.58 Chain J: Q.58 Ligands: NA.9, NA.33, CL.34, NA.57, CL.58 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: T.16 Chain B: T.16 Chain C: T.16 Ligands: CL.5, CL.17 Ligand excluded by PLIP CL.16: 8 residues within 4Å: Chain C: Q.58 Chain E: Q.58 Chain G: Q.58 Ligands: NA.15, NA.27, CL.28, NA.39, CL.40 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain A: T.16 Chain B: T.16 Chain C: T.16 Ligands: CL.5, CL.11 Ligand excluded by PLIP CL.22: 8 residues within 4Å: Chain D: Q.58 Chain H: Q.58 Chain L: Q.58 Ligands: NA.21, NA.45, CL.46, NA.69, CL.70 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain D: T.16 Chain E: T.16 Chain F: T.16 Ligands: CL.29, CL.35 Ligand excluded by PLIP CL.28: 8 residues within 4Å: Chain C: Q.58 Chain E: Q.58 Chain G: Q.58 Ligands: NA.15, CL.16, NA.27, NA.39, CL.40 Ligand excluded by PLIP CL.29: 5 residues within 4Å: Chain D: T.16 Chain E: T.16 Chain F: T.16 Ligands: CL.23, CL.35 Ligand excluded by PLIP CL.34: 8 residues within 4Å: Chain B: Q.58 Chain F: Q.58 Chain J: Q.58 Ligands: NA.9, CL.10, NA.33, NA.57, CL.58 Ligand excluded by PLIP CL.35: 5 residues within 4Å: Chain D: T.16 Chain E: T.16 Chain F: T.16 Ligands: CL.23, CL.29 Ligand excluded by PLIP CL.40: 8 residues within 4Å: Chain C: Q.58 Chain E: Q.58 Chain G: Q.58 Ligands: NA.15, CL.16, NA.27, CL.28, NA.39 Ligand excluded by PLIP CL.41: 5 residues within 4Å: Chain G: T.16 Chain H: T.16 Chain I: T.16 Ligands: CL.47, CL.53 Ligand excluded by PLIP CL.46: 8 residues within 4Å: Chain D: Q.58 Chain H: Q.58 Chain L: Q.58 Ligands: NA.21, CL.22, NA.45, NA.69, CL.70 Ligand excluded by PLIP CL.47: 5 residues within 4Å: Chain G: T.16 Chain H: T.16 Chain I: T.16 Ligands: CL.41, CL.53 Ligand excluded by PLIP CL.52: 8 residues within 4Å: Chain A: Q.58 Chain I: Q.58 Chain K: Q.58 Ligands: NA.3, CL.4, NA.51, NA.63, CL.64 Ligand excluded by PLIP CL.53: 5 residues within 4Å: Chain G: T.16 Chain H: T.16 Chain I: T.16 Ligands: CL.41, CL.47 Ligand excluded by PLIP CL.58: 8 residues within 4Å: Chain B: Q.58 Chain F: Q.58 Chain J: Q.58 Ligands: NA.9, CL.10, NA.33, CL.34, NA.57 Ligand excluded by PLIP CL.59: 5 residues within 4Å: Chain J: T.16 Chain K: T.16 Chain L: T.16 Ligands: CL.65, CL.71 Ligand excluded by PLIP CL.64: 8 residues within 4Å: Chain A: Q.58 Chain I: Q.58 Chain K: Q.58 Ligands: NA.3, CL.4, NA.51, CL.52, NA.63 Ligand excluded by PLIP CL.65: 5 residues within 4Å: Chain J: T.16 Chain K: T.16 Chain L: T.16 Ligands: CL.59, CL.71 Ligand excluded by PLIP CL.70: 8 residues within 4Å: Chain D: Q.58 Chain H: Q.58 Chain L: Q.58 Ligands: NA.21, CL.22, NA.45, CL.46, NA.69 Ligand excluded by PLIP CL.71: 5 residues within 4Å: Chain J: T.16 Chain K: T.16 Chain L: T.16 Ligands: CL.59, CL.65 Ligand excluded by PLIP

12 x RBF: RIBOFLAVIN(Non-covalent)

RBF.6: 15 residues within 4Å: Chain A: F.2, V.34, W.35, A.36, E.37 Chain B: G.42, V.43, E.44, G.46, A.47, Q.54 Chain K: E.44, A.47, Q.54 Ligands: RBF.60 10 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B, 2 interactions with chain K Hydrophobic interactions: A:W.35, A:E.37 Water bridges: A:K.4 pi-Stacking: A:W.35, A:W.35, A:W.35, A:W.35 Hydrogen bonds: B:E.44, K:Q.54, K:Q.54 RBF.12: 15 residues within 4Å: Chain B: F.2, V.34, W.35, A.36, E.37 Chain C: G.42, V.43, E.44, G.46, A.47, Q.54 Chain F: E.44, A.47, Q.54 Ligands: RBF.30 10 PLIP interactions: 7 interactions with chain B, 2 interactions with chain F, 1 interactions with chain C Hydrophobic interactions: B:W.35, B:E.37 Water bridges: B:K.4 pi-Stacking: B:W.35, B:W.35, B:W.35, B:W.35 Hydrogen bonds: F:Q.54, F:Q.54, C:E.44 RBF.18: 15 residues within 4Å: Chain A: G.42, V.43, E.44, G.46, A.47, Q.54 Chain C: F.2, V.34, W.35, A.36, E.37 Chain G: E.44, A.47, Q.54 Ligands: RBF.54 11 PLIP interactions: 3 interactions with chain G, 7 interactions with chain C, 1 interactions with chain A Hydrogen bonds: G:E.44, G:Q.54, G:Q.54, A:E.44 Hydrophobic interactions: C:W.35, C:E.37 Water bridges: C:K.4 pi-Stacking: C:W.35, C:W.35, C:W.35, C:W.35 RBF.24: 15 residues within 4Å: Chain D: F.2, V.34, W.35, A.36, E.37 Chain E: G.42, V.43, E.44, G.46, A.47, Q.54 Chain H: E.44, A.47, Q.54 Ligands: RBF.42 10 PLIP interactions: 1 interactions with chain E, 7 interactions with chain D, 2 interactions with chain H Hydrogen bonds: E:E.44, H:Q.54, H:Q.54 Hydrophobic interactions: D:W.35, D:E.37 Water bridges: D:K.4 pi-Stacking: D:W.35, D:W.35, D:W.35, D:W.35 RBF.30: 15 residues within 4Å: Chain C: E.44, A.47, Q.54 Chain E: F.2, V.34, W.35, A.36, E.37 Chain F: G.42, V.43, E.44, G.46, A.47, Q.54 Ligands: RBF.12 10 PLIP interactions: 1 interactions with chain F, 7 interactions with chain E, 2 interactions with chain C Hydrogen bonds: F:E.44, C:Q.54, C:Q.54 Hydrophobic interactions: E:W.35, E:E.37 Water bridges: E:K.4 pi-Stacking: E:W.35, E:W.35, E:W.35, E:W.35 RBF.36: 15 residues within 4Å: Chain D: G.42, V.43, E.44, G.46, A.47, Q.54 Chain F: F.2, V.34, W.35, A.36, E.37 Chain J: E.44, A.47, Q.54 Ligands: RBF.72 11 PLIP interactions: 7 interactions with chain F, 3 interactions with chain J, 1 interactions with chain D Hydrophobic interactions: F:W.35, F:E.37 Water bridges: F:K.4 pi-Stacking: F:W.35, F:W.35, F:W.35, F:W.35 Hydrogen bonds: J:E.44, J:Q.54, J:Q.54, D:E.44 RBF.42: 15 residues within 4Å: Chain E: E.44, A.47, Q.54 Chain G: F.2, V.34, W.35, A.36, E.37 Chain H: G.42, V.43, E.44, G.46, A.47, Q.54 Ligands: RBF.24 11 PLIP interactions: 7 interactions with chain G, 3 interactions with chain E, 1 interactions with chain H Hydrophobic interactions: G:W.35, G:E.37 Water bridges: G:K.4 pi-Stacking: G:W.35, G:W.35, G:W.35, G:W.35 Hydrogen bonds: E:E.44, E:Q.54, E:Q.54, H:E.44 RBF.48: 15 residues within 4Å: Chain H: F.2, V.34, W.35, A.36, E.37 Chain I: G.42, V.43, E.44, G.46, A.47, Q.54 Chain L: E.44, A.47, Q.54 Ligands: RBF.66 11 PLIP interactions: 3 interactions with chain L, 1 interactions with chain I, 7 interactions with chain H Hydrogen bonds: L:E.44, L:Q.54, L:Q.54, I:E.44 Hydrophobic interactions: H:W.35, H:E.37 Water bridges: H:K.4 pi-Stacking: H:W.35, H:W.35, H:W.35, H:W.35 RBF.54: 15 residues within 4Å: Chain A: E.44, A.47, Q.54 Chain G: G.42, V.43, E.44, G.46, A.47, Q.54 Chain I: F.2, V.34, W.35, A.36, E.37 Ligands: RBF.18 10 PLIP interactions: 1 interactions with chain G, 7 interactions with chain I, 2 interactions with chain A Hydrogen bonds: G:E.44, A:Q.54, A:Q.54 Hydrophobic interactions: I:W.35, I:E.37 Water bridges: I:K.4 pi-Stacking: I:W.35, I:W.35, I:W.35, I:W.35 RBF.60: 15 residues within 4Å: Chain B: E.44, A.47, Q.54 Chain J: F.2, V.34, W.35, A.36, E.37 Chain K: G.42, V.43, E.44, G.46, A.47, Q.54 Ligands: RBF.6 11 PLIP interactions: 1 interactions with chain K, 7 interactions with chain J, 3 interactions with chain B Hydrogen bonds: K:E.44, B:E.44, B:Q.54, B:Q.54 Hydrophobic interactions: J:W.35, J:E.37 Water bridges: J:K.4 pi-Stacking: J:W.35, J:W.35, J:W.35, J:W.35 RBF.66: 15 residues within 4Å: Chain I: E.44, A.47, Q.54 Chain K: F.2, V.34, W.35, A.36, E.37 Chain L: G.42, V.43, E.44, G.46, A.47, Q.54 Ligands: RBF.48 11 PLIP interactions: 3 interactions with chain I, 7 interactions with chain K, 1 interactions with chain L Hydrogen bonds: I:E.44, I:Q.54, I:Q.54, L:E.44 Hydrophobic interactions: K:W.35, K:E.37 Water bridges: K:K.4 pi-Stacking: K:W.35, K:W.35, K:W.35, K:W.35 RBF.72: 15 residues within 4Å: Chain D: E.44, A.47, Q.54 Chain J: G.42, V.43, E.44, G.46, A.47, Q.54 Chain L: F.2, V.34, W.35, A.36, E.37 Ligands: RBF.36 10 PLIP interactions: 7 interactions with chain L, 2 interactions with chain D, 1 interactions with chain J Hydrophobic interactions: L:W.35, L:E.37 Water bridges: L:K.4 pi-Stacking: L:W.35, L:W.35, L:W.35, L:W.35 Hydrogen bonds: D:Q.54, D:Q.54, J:E.44

Links

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Citation

Bieger, B. et al., Crystal Structure of Halophilic Dodecin: A Novel, Dodecameric Flavin Binding Protein from Halobacterium salinarum. Structure (2003)

Release Date

2003-04-15

Peptides

Dodecin: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

Dodecin