SMTL ID : 2v18.1

Crystal structure of the T. thermophilus dodecin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

homo-12-mer

Ligands

12 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 13 residues within 4Å: Chain A: K.2, Y.4, D.36, W.37, R.64 Chain B: R.44, T.46, Q.56 Chain H: V.10, R.44, Q.56, V.58 Ligands: FMN.12 14 PLIP interactions: 3 interactions with chain B, 1 interactions with chain H, 10 interactions with chain A Hydrogen bonds: B:R.44, B:Q.56, B:Q.56, A:Y.4, A:Y.4, A:D.36 Hydrophobic interactions: H:V.58, A:Y.4, A:W.37, A:W.37 Salt bridges: A:R.64 pi-Stacking: A:W.37, A:W.37, A:W.37 FMN.2: 13 residues within 4Å: Chain B: K.2, Y.4, D.36, W.37, R.64 Chain C: R.44, T.46, Q.56 Chain F: V.10, R.44, Q.56, V.58 Ligands: FMN.8 13 PLIP interactions: 3 interactions with chain C, 9 interactions with chain B, 1 interactions with chain F Hydrogen bonds: C:R.44, C:Q.56, C:Q.56, B:Y.4, B:Y.4, B:D.36 Hydrophobic interactions: B:W.37, B:W.37, F:V.58 Salt bridges: B:R.64 pi-Stacking: B:W.37, B:W.37, B:W.37 FMN.4: 13 residues within 4Å: Chain A: R.44, T.46, Q.56 Chain C: K.2, Y.4, D.36, W.37, R.64 Chain J: V.10, R.44, Q.56, V.58 Ligands: FMN.21 13 PLIP interactions: 3 interactions with chain A, 1 interactions with chain J, 9 interactions with chain C Hydrogen bonds: A:R.44, A:Q.56, A:Q.56, C:Y.4, C:D.36 Hydrophobic interactions: J:V.58, C:Y.4, C:W.37, C:W.37 Salt bridges: C:R.64 pi-Stacking: C:W.37, C:W.37, C:W.37 FMN.6: 13 residues within 4Å: Chain D: K.2, Y.4, D.36, W.37, R.64 Chain E: R.44, T.46, Q.56 Chain K: V.10, R.44, Q.56, V.58 Ligands: FMN.17 13 PLIP interactions: 3 interactions with chain E, 9 interactions with chain D, 1 interactions with chain K Hydrogen bonds: E:R.44, E:Q.56, E:Q.56, D:Y.4, D:D.36 Hydrophobic interactions: D:Y.4, D:W.37, D:W.37, K:V.58 Salt bridges: D:R.64 pi-Stacking: D:W.37, D:W.37, D:W.37 FMN.8: 13 residues within 4Å: Chain C: V.10, R.44, Q.56, V.58 Chain E: K.2, Y.4, D.36, W.37, R.64 Chain F: R.44, T.46, Q.56 Ligands: FMN.2 13 PLIP interactions: 9 interactions with chain E, 1 interactions with chain C, 3 interactions with chain F Hydrophobic interactions: E:Y.4, E:W.37, E:W.37, C:V.58 Hydrogen bonds: E:Y.4, E:D.36, E:R.64, F:R.44, F:Q.56, F:Q.56 pi-Stacking: E:W.37, E:W.37, E:W.37 FMN.10: 13 residues within 4Å: Chain D: R.44, T.46, Q.56 Chain F: K.2, Y.4, D.36, W.37, R.64 Chain G: V.10, R.44, Q.56, V.58 Ligands: FMN.15 13 PLIP interactions: 9 interactions with chain F, 3 interactions with chain D, 1 interactions with chain G Hydrophobic interactions: F:Y.4, F:W.37, F:W.37, G:V.58 Hydrogen bonds: F:Y.4, F:D.36, D:R.44, D:Q.56, D:Q.56 Salt bridges: F:R.64 pi-Stacking: F:W.37, F:W.37, F:W.37 FMN.12: 13 residues within 4Å: Chain B: V.10, R.44, Q.56, V.58 Chain G: K.2, Y.4, D.36, W.37, R.64 Chain H: R.44, T.46, Q.56 Ligands: FMN.1 13 PLIP interactions: 9 interactions with chain G, 3 interactions with chain H, 1 interactions with chain B Hydrophobic interactions: G:Y.4, G:W.37, G:W.37, B:V.58 Hydrogen bonds: G:Y.4, G:D.36, H:R.44, H:Q.56, H:Q.56 Salt bridges: G:R.64 pi-Stacking: G:W.37, G:W.37, G:W.37 FMN.14: 13 residues within 4Å: Chain H: K.2, Y.4, D.36, W.37, R.64 Chain I: R.44, T.46, Q.56 Chain L: V.10, R.44, Q.56, V.58 Ligands: FMN.19 14 PLIP interactions: 10 interactions with chain H, 3 interactions with chain I, 1 interactions with chain L Hydrophobic interactions: H:Y.4, H:W.37, H:W.37, L:V.58 Hydrogen bonds: H:Y.4, H:Y.4, H:D.36, I:R.44, I:Q.56, I:Q.56 Salt bridges: H:R.64 pi-Stacking: H:W.37, H:W.37, H:W.37 FMN.15: 13 residues within 4Å: Chain D: V.10, R.44, Q.56, V.58 Chain G: R.44, T.46, Q.56 Chain I: K.2, Y.4, D.36, W.37, R.64 Ligands: FMN.10 13 PLIP interactions: 1 interactions with chain D, 3 interactions with chain G, 9 interactions with chain I Hydrophobic interactions: D:V.58, I:W.37, I:W.37 Hydrogen bonds: G:R.44, G:Q.56, G:Q.56, I:Y.4, I:Y.4, I:D.36 Salt bridges: I:R.64 pi-Stacking: I:W.37, I:W.37, I:W.37 FMN.17: 13 residues within 4Å: Chain E: V.10, R.44, Q.56, V.58 Chain J: K.2, Y.4, D.36, W.37, R.64 Chain K: R.44, T.46, Q.56 Ligands: FMN.6 13 PLIP interactions: 9 interactions with chain J, 3 interactions with chain K, 1 interactions with chain E Hydrophobic interactions: J:W.37, J:W.37, E:V.58 Hydrogen bonds: J:Y.4, J:Y.4, J:D.36, K:R.44, K:Q.56, K:Q.56 Salt bridges: J:R.64 pi-Stacking: J:W.37, J:W.37, J:W.37 FMN.19: 13 residues within 4Å: Chain I: V.10, R.44, Q.56, V.58 Chain K: K.2, Y.4, D.36, W.37, R.64 Chain L: R.44, T.46, Q.56 Ligands: FMN.14 14 PLIP interactions: 1 interactions with chain I, 10 interactions with chain K, 3 interactions with chain L Hydrophobic interactions: I:V.58, K:Y.4, K:W.37, K:W.37 Hydrogen bonds: K:Y.4, K:Y.4, K:D.36, L:R.44, L:Q.56, L:Q.56 Salt bridges: K:R.64 pi-Stacking: K:W.37, K:W.37, K:W.37 FMN.21: 13 residues within 4Å: Chain A: V.10, R.44, Q.56, V.58 Chain J: R.44, T.46, Q.56 Chain L: K.2, Y.4, D.36, W.37, R.64 Ligands: FMN.4 14 PLIP interactions: 10 interactions with chain L, 3 interactions with chain J, 1 interactions with chain A Hydrophobic interactions: L:Y.4, L:W.37, L:W.37, A:V.58 Hydrogen bonds: L:Y.4, L:Y.4, L:D.36, J:R.44, J:Q.56, J:Q.56 Salt bridges: L:R.64 pi-Stacking: L:W.37, L:W.37, L:W.37

9 x COA: COENZYME A(Non-covalent)

COA.3: 20 residues within 4Å: Chain B: R.27, T.31, L.32, R.33, H.34, F.63, R.64, L.65, E.66 Chain F: K.5, L.65 Chain G: K.5, V.7, R.27, A.28, L.32, F.63, L.65 Ligands: COA.11, COA.13 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain G Hydrogen bonds: B:T.31, B:T.31, B:R.33, B:R.33, B:R.33, B:R.33, B:E.66, G:K.5 Salt bridges: B:R.27 pi-Cation interactions: B:R.33 Hydrophobic interactions: G:K.5, G:F.63, G:L.65 COA.5: 21 residues within 4Å: Chain C: R.27, T.31, L.32, R.33, H.34, F.63, R.64, L.65, E.66 Chain E: K.5, V.7, L.9, R.27, A.28, L.32, F.63, L.65 Chain J: K.5, L.65 Ligands: COA.9, COA.18 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain E Hydrogen bonds: C:T.31, C:R.33, C:R.33, C:R.33, C:R.33, C:E.66, E:K.5 Salt bridges: C:R.27 pi-Cation interactions: C:R.33 Hydrophobic interactions: E:K.5, E:L.32, E:L.65 COA.7: 20 residues within 4Å: Chain D: R.27, T.31, L.32, R.33, H.34, F.63, R.64, L.65, E.66 Chain I: K.5, V.7, R.27, A.28, T.31, L.32, L.65 Chain K: K.5, L.65 Ligands: COA.16, COA.20 13 PLIP interactions: 9 interactions with chain D, 4 interactions with chain I Hydrogen bonds: D:T.31, D:T.31, D:R.33, D:R.33, D:R.33, D:R.64, D:E.66, I:K.5 Salt bridges: D:R.27 pi-Cation interactions: D:R.33 Hydrophobic interactions: I:K.5, I:L.32, I:L.65 COA.9: 20 residues within 4Å: Chain C: K.5 Chain E: R.27, T.31, L.32, R.33, H.34, F.63, R.64, L.65, E.66 Chain J: K.5, V.7, L.9, A.28, T.31, L.32, F.63, L.65 Ligands: COA.5, COA.18 13 PLIP interactions: 4 interactions with chain J, 9 interactions with chain E Hydrophobic interactions: J:L.32, J:F.63, J:L.65 Hydrogen bonds: J:K.5, E:T.31, E:T.31, E:R.33, E:R.33, E:R.33, E:R.64, E:E.66 Salt bridges: E:R.27 pi-Cation interactions: E:R.33 COA.11: 22 residues within 4Å: Chain B: K.5, V.7, L.9, R.27, A.28, T.31, L.32, F.63, L.65 Chain F: R.27, T.31, L.32, R.33, H.34, F.63, R.64, L.65, E.66 Chain G: K.5, L.65 Ligands: COA.3, COA.13 13 PLIP interactions: 9 interactions with chain F, 4 interactions with chain B Hydrogen bonds: F:T.31, F:T.31, F:R.33, F:R.33, F:R.33, F:R.33, F:E.66, B:K.5 Salt bridges: F:R.27 pi-Cation interactions: F:R.33 Hydrophobic interactions: B:K.5, B:L.32, B:L.65 COA.13: 21 residues within 4Å: Chain B: K.5, L.65 Chain F: K.5, V.7, L.9, R.27, T.31, L.32, F.63, L.65 Chain G: R.27, T.31, L.32, R.33, H.34, F.63, R.64, L.65, E.66 Ligands: COA.3, COA.11 11 PLIP interactions: 8 interactions with chain G, 3 interactions with chain F Hydrogen bonds: G:T.31, G:R.33, G:R.33, G:R.33, G:R.64, G:E.66, F:K.5 Salt bridges: G:R.27 pi-Cation interactions: G:R.33 Hydrophobic interactions: F:L.32, F:L.65 COA.16: 20 residues within 4Å: Chain D: K.5, L.65 Chain I: R.27, T.31, L.32, R.33, H.34, F.63, R.64, L.65, E.66 Chain K: K.5, V.7, L.9, A.28, L.32, F.63, L.65 Ligands: COA.7, COA.20 14 PLIP interactions: 9 interactions with chain I, 5 interactions with chain K Hydrogen bonds: I:T.31, I:T.31, I:R.33, I:R.33, I:R.33, I:R.64, I:E.66, K:K.5 Salt bridges: I:R.27 pi-Cation interactions: I:R.33 Hydrophobic interactions: K:K.5, K:L.32, K:F.63, K:L.65 COA.18: 21 residues within 4Å: Chain C: K.5, V.7, L.9, A.28, T.31, L.32, F.63, L.65 Chain E: K.5, L.65 Chain J: R.27, T.31, L.32, R.33, H.34, F.63, R.64, L.65, E.66 Ligands: COA.5, COA.9 13 PLIP interactions: 8 interactions with chain J, 5 interactions with chain C Hydrogen bonds: J:T.31, J:R.33, J:R.33, J:R.33, J:R.64, J:E.66, C:K.5 Salt bridges: J:R.27 pi-Cation interactions: J:R.33 Hydrophobic interactions: C:K.5, C:L.32, C:F.63, C:L.65 COA.20: 21 residues within 4Å: Chain D: K.5, V.7, L.9, R.27, A.28, T.31, L.32, L.65 Chain I: K.5, L.65 Chain K: R.27, T.31, L.32, R.33, H.34, F.63, R.64, L.65, E.66 Ligands: COA.7, COA.16 11 PLIP interactions: 8 interactions with chain K, 3 interactions with chain D Hydrogen bonds: K:T.31, K:R.33, K:R.33, K:R.33, K:R.64, K:E.66, D:K.5 Salt bridges: K:R.27 pi-Cation interactions: K:R.33 Hydrophobic interactions: D:K.5, D:L.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meissner, B. et al., The Dodecin from Thermus Thermophilus, a Bifunctional Cofactor Storage Protein. J.Biol.Chem. (2007)

Release Date

2007-09-11

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