SMTL ID : 2vxa.1

H. halophila dodecin in complex with riboflavin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-12-mer

Ligands

12 x RBF: RIBOFLAVIN(Non-covalent)

RBF.1: 10 residues within 4Å: Chain A: Y.6, R.38, W.39 Chain C: R.46, Q.58 Chain E: R.46, G.47, H.48, Q.58 Ligands: RBF.18 12 PLIP interactions: 4 interactions with chain E, 7 interactions with chain A, 1 interactions with chain C Hydrogen bonds: E:R.46, E:H.48, E:Q.58, E:Q.58, A:Y.6, A:R.38 Hydrophobic interactions: A:Y.6, A:W.39, C:Q.58 pi-Stacking: A:W.39, A:W.39, A:W.39 RBF.4: 10 residues within 4Å: Chain A: R.46, Q.58 Chain B: Y.6, R.38, W.39 Chain K: R.46, H.48, Q.58 Ligands: CL.34, RBF.36 10 PLIP interactions: 5 interactions with chain B, 4 interactions with chain K, 1 interactions with chain A Hydrophobic interactions: B:W.39, A:Q.58 Hydrogen bonds: B:R.38, K:R.46, K:H.48, K:Q.58, K:Q.58 pi-Stacking: B:W.39, B:W.39, B:W.39 RBF.7: 10 residues within 4Å: Chain B: R.46, Q.58 Chain C: Y.6, R.38, W.39 Chain G: R.46, H.48, Q.58 Ligands: CL.21, RBF.25 12 PLIP interactions: 1 interactions with chain B, 7 interactions with chain C, 4 interactions with chain G Hydrophobic interactions: B:Q.58, C:Y.6, C:W.39 Hydrogen bonds: C:Y.6, C:R.38, G:R.46, G:H.48, G:Q.58, G:Q.58 pi-Stacking: C:W.39, C:W.39, C:W.39 RBF.10: 10 residues within 4Å: Chain D: Y.6, R.38, W.39 Chain F: R.46, Q.58 Chain I: R.46, H.48, Q.58 Ligands: RBF.20, CL.28 11 PLIP interactions: 1 interactions with chain F, 4 interactions with chain I, 6 interactions with chain D Hydrophobic interactions: F:Q.58, D:Y.6, D:W.39 Hydrogen bonds: I:R.46, I:H.48, I:Q.58, I:Q.58, D:R.38 pi-Stacking: D:W.39, D:W.39, D:W.39 RBF.14: 10 residues within 4Å: Chain D: R.46, Q.58 Chain E: Y.6, R.38, W.39 Chain L: R.46, H.48, Q.58 Ligands: CL.16, RBF.30 12 PLIP interactions: 7 interactions with chain E, 4 interactions with chain L, 1 interactions with chain D Hydrophobic interactions: E:Y.6, E:W.39, D:Q.58 Hydrogen bonds: E:Y.6, E:R.38, L:R.46, L:H.48, L:Q.58, L:Q.58 pi-Stacking: E:W.39, E:W.39, E:W.39 RBF.18: 12 residues within 4Å: Chain C: R.46, G.47, H.48, Q.58 Chain E: T.12, R.46, Q.58 Chain F: Y.6, R.38, W.39 Ligands: RBF.1, CL.8 13 PLIP interactions: 1 interactions with chain E, 4 interactions with chain C, 8 interactions with chain F Hydrophobic interactions: E:Q.58, F:Y.6, F:W.39, F:W.39 Hydrogen bonds: C:R.46, C:H.48, C:Q.58, C:Q.58, F:Y.6, F:R.38 pi-Stacking: F:W.39, F:W.39, F:W.39 RBF.20: 9 residues within 4Å: Chain F: R.46, H.48, Q.58 Chain G: Y.6, R.38, W.39 Chain I: T.12, Q.58 Ligands: RBF.10 12 PLIP interactions: 7 interactions with chain G, 4 interactions with chain F, 1 interactions with chain I Hydrophobic interactions: G:Y.6, G:W.39, I:Q.58 Hydrogen bonds: G:Y.6, G:R.38, F:R.46, F:H.48, F:Q.58, F:Q.58 pi-Stacking: G:W.39, G:W.39, G:W.39 RBF.25: 11 residues within 4Å: Chain B: R.46, G.47, H.48, Q.58 Chain G: R.46, Q.58 Chain H: Y.6, R.38, W.39 Ligands: CL.5, RBF.7 11 PLIP interactions: 6 interactions with chain H, 4 interactions with chain B, 1 interactions with chain G Hydrophobic interactions: H:Y.6, H:W.39, G:Q.58 Hydrogen bonds: H:R.38, B:R.46, B:H.48, B:Q.58, B:Q.58 pi-Stacking: H:W.39, H:W.39, H:W.39 RBF.27: 10 residues within 4Å: Chain H: R.46, Q.58 Chain I: Y.6, R.38, W.39 Chain J: R.46, H.48, Q.58 Ligands: CL.31, RBF.33 11 PLIP interactions: 6 interactions with chain I, 4 interactions with chain J, 1 interactions with chain H Hydrophobic interactions: I:Y.6, I:W.39, H:Q.58 Hydrogen bonds: I:R.38, J:R.46, J:H.48, J:Q.58, J:Q.58 pi-Stacking: I:W.39, I:W.39, I:W.39 RBF.30: 9 residues within 4Å: Chain D: R.46, H.48, Q.58 Chain J: Y.6, R.38, W.39 Chain L: R.46, Q.58 Ligands: RBF.14 11 PLIP interactions: 4 interactions with chain D, 1 interactions with chain L, 6 interactions with chain J Hydrogen bonds: D:R.46, D:H.48, D:Q.58, D:Q.58, J:R.38 Hydrophobic interactions: L:Q.58, J:Y.6, J:W.39 pi-Stacking: J:W.39, J:W.39, J:W.39 RBF.33: 11 residues within 4Å: Chain H: R.46, G.47, H.48, Q.58 Chain J: R.46, Q.58 Chain K: Y.6, R.38, W.39 Ligands: CL.26, RBF.27 11 PLIP interactions: 6 interactions with chain K, 4 interactions with chain H, 1 interactions with chain J Hydrophobic interactions: K:Y.6, K:W.39, J:Q.58 Hydrogen bonds: K:R.38, H:R.46, H:H.48, H:Q.58, H:Q.58 pi-Stacking: K:W.39, K:W.39, K:W.39 RBF.36: 10 residues within 4Å: Chain A: R.46, G.47, H.48, Q.58 Chain K: R.46, Q.58 Chain L: Y.6, R.38, W.39 Ligands: RBF.4 12 PLIP interactions: 7 interactions with chain L, 4 interactions with chain A, 1 interactions with chain K Hydrophobic interactions: L:Y.6, L:W.39, K:Q.58 Hydrogen bonds: L:Y.6, L:R.38, A:R.46, A:H.48, A:Q.58, A:Q.58 pi-Stacking: L:W.39, L:W.39, L:W.39

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

CL.2: 5 residues within 4Å: Chain A: K.7, V.9 Chain B: K.7, V.9 Chain C: K.7 Ligand excluded by PLIP CL.3: 6 residues within 4Å: Chain A: E.10, K.62 Chain B: E.10, K.62 Chain C: E.10, K.62 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain B: R.46 Chain H: W.39 Ligands: RBF.25 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain B: S.14, H.56, Q.58 Chain C: H.4, Y.6 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain C: R.46 Chain F: W.39 Ligands: RBF.18 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain A: H.4, Y.6 Chain C: S.14, H.56, Q.58 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain D: H.4, Y.6 Chain F: S.14, Q.58 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain D: S.14, H.56, Q.58 Chain E: Y.6 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain D: E.10, K.62 Chain E: E.10, K.62 Chain F: E.10, K.62 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: W.39 Chain E: R.46 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain E: W.39 Chain L: R.46 Ligands: RBF.14 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain E: S.14, H.56, Q.58 Chain F: H.4, Y.6 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain F: R.46 Chain G: W.39 Chain I: D.44, R.46 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain C: W.39 Chain G: R.46 Ligands: RBF.7 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain G: S.14, H.56, Q.58 Chain H: Y.6 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain G: Y.6 Chain I: S.14, Q.58 Ligand excluded by PLIP CL.24: 6 residues within 4Å: Chain G: E.10, K.62 Chain H: E.10, K.62 Chain I: E.10, K.62 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain H: R.46 Chain K: W.39 Ligands: RBF.33 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain D: W.39 Chain I: R.46 Ligands: RBF.10 Ligand excluded by PLIP CL.29: 5 residues within 4Å: Chain H: S.14, H.56, Q.58 Chain I: H.4, Y.6 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain I: W.39 Chain J: R.46 Ligands: RBF.27 Ligand excluded by PLIP CL.32: 6 residues within 4Å: Chain J: E.10, K.62 Chain K: E.10, K.62 Chain L: E.10, K.62 Ligand excluded by PLIP CL.34: 3 residues within 4Å: Chain B: W.39 Chain K: R.46 Ligands: RBF.4 Ligand excluded by PLIP CL.35: 4 residues within 4Å: Chain J: S.14, Q.58 Chain K: H.4, Y.6 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grininger, M. et al., Dodecin is the Key Player in Flavin Homeostasis of Archaea. J.Biol.Chem. (2009)

Release Date

2009-02-17

Peptides

DODECIN: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

DODECIN