SMTL ID : 2ux9.1

Crystal structure of the T. thermophilus dodecin R65A mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-12-mer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: H.35, A.65 Ligands: FMN.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.35 NA.8: 4 residues within 4Å: Chain C: T.13, E.55 Chain G: G.2, K.3 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain G Hydrogen bonds: C:T.13, G:K.3 Water bridges: C:T.13, C:E.15 NA.9: 3 residues within 4Å: Chain C: H.35, D.37 Ligands: FMN.10 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.37 NA.17: 1 residues within 4Å: Ligands: FMN.15 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:H.35 NA.20: 3 residues within 4Å: Chain G: H.35, A.65 Ligands: FMN.21 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:H.35 NA.27: 4 residues within 4Å: Chain A: G.2, K.3 Chain I: T.13, E.55 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain A Hydrogen bonds: I:T.13, I:E.55, A:K.3 Water bridges: I:E.15 NA.28: 3 residues within 4Å: Chain I: H.35, D.37 Ligands: FMN.29 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:H.35, I:D.37 NA.36: 1 residues within 4Å: Ligands: FMN.34 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:H.35

12 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 14 residues within 4Å: Chain A: K.3, Y.5, D.37, W.38, A.65 Chain C: R.45, T.47, Q.57 Chain I: V.11, R.45, Q.57, V.59 Ligands: NA.1, FMN.21 12 PLIP interactions: 2 interactions with chain I, 7 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: I:V.59, A:W.38, A:W.38 Water bridges: I:Q.57 Hydrogen bonds: A:Y.5, C:R.45, C:Q.57, C:Q.57 Salt bridges: A:K.3 pi-Stacking: A:W.38, A:W.38, A:W.38 FMN.5: 13 residues within 4Å: Chain B: K.3, Y.5, D.37, W.38, A.65 Chain D: R.45, T.47, Q.57 Chain J: V.11, R.45, Q.57, V.59 Ligands: FMN.24 15 PLIP interactions: 3 interactions with chain D, 3 interactions with chain J, 9 interactions with chain B Hydrogen bonds: D:R.45, D:Q.57, D:Q.57, B:Y.5, B:Y.5 Hydrophobic interactions: J:V.11, J:V.59, B:W.38, B:W.38 Water bridges: J:Q.57, B:D.37 Salt bridges: B:K.3 pi-Stacking: B:W.38, B:W.38, B:W.38 FMN.10: 14 residues within 4Å: Chain C: K.3, Y.5, D.37, W.38, A.65 Chain F: R.45, T.47, Q.57 Chain K: V.11, R.45, Q.57, V.59 Ligands: NA.9, FMN.31 16 PLIP interactions: 10 interactions with chain C, 3 interactions with chain F, 3 interactions with chain K Hydrophobic interactions: C:Y.5, C:W.38, C:W.38, K:V.59 Hydrogen bonds: C:Y.5, F:R.45, F:Q.57, F:Q.57 Water bridges: C:K.3, C:D.37, K:Q.57, K:Q.57 Salt bridges: C:K.3 pi-Stacking: C:W.38, C:W.38, C:W.38 FMN.12: 12 residues within 4Å: Chain D: K.3, Y.5, D.37, W.38, A.65 Chain E: R.45, T.47, Q.57 Chain L: V.11, R.45, Q.57 Ligands: FMN.29 17 PLIP interactions: 12 interactions with chain D, 2 interactions with chain L, 3 interactions with chain E Hydrophobic interactions: D:Y.5, D:W.38, D:W.38, L:V.11 Hydrogen bonds: D:Y.5, D:Y.5, E:R.45, E:Q.57, E:Q.57 Water bridges: D:K.3, D:K.3, D:D.37, L:Q.57 Salt bridges: D:K.3 pi-Stacking: D:W.38, D:W.38, D:W.38 FMN.14: 13 residues within 4Å: Chain A: V.11, R.45, Q.57, V.59 Chain B: R.45, T.47, Q.57 Chain E: K.3, Y.5, D.37, W.38, A.65 Ligands: FMN.15 17 PLIP interactions: 12 interactions with chain E, 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: E:Y.5, E:W.38, E:W.38, A:V.59 Hydrogen bonds: E:Y.5, E:Y.5, B:R.45, B:Q.57, B:Q.57 Water bridges: E:K.3, E:D.37, E:D.37, A:Q.57 Salt bridges: E:K.3 pi-Stacking: E:W.38, E:W.38, E:W.38 FMN.15: 14 residues within 4Å: Chain A: R.45, T.47, Q.57 Chain B: V.11, R.45, Q.57, V.59 Chain F: K.3, Y.5, D.37, W.38, A.65 Ligands: FMN.14, NA.17 13 PLIP interactions: 3 interactions with chain A, 8 interactions with chain F, 2 interactions with chain B Hydrogen bonds: A:R.45, A:Q.57, A:Q.57, F:Y.5 Hydrophobic interactions: F:W.38, F:W.38, B:V.59 Water bridges: F:K.3, B:Q.57 Salt bridges: F:K.3 pi-Stacking: F:W.38, F:W.38, F:W.38 FMN.21: 14 residues within 4Å: Chain C: V.11, R.45, Q.57, V.59 Chain G: K.3, Y.5, D.37, W.38, A.65 Chain I: R.45, T.47, Q.57 Ligands: FMN.2, NA.20 13 PLIP interactions: 3 interactions with chain I, 2 interactions with chain C, 8 interactions with chain G Hydrogen bonds: I:R.45, I:Q.57, I:Q.57, G:Y.5, G:Y.5 Hydrophobic interactions: C:V.59, G:W.38, G:W.38 Water bridges: C:Q.57 Salt bridges: G:K.3 pi-Stacking: G:W.38, G:W.38, G:W.38 FMN.24: 13 residues within 4Å: Chain D: V.11, R.45, Q.57, V.59 Chain H: K.3, Y.5, D.37, W.38, A.65 Chain J: R.45, T.47, Q.57 Ligands: FMN.5 14 PLIP interactions: 8 interactions with chain H, 3 interactions with chain D, 3 interactions with chain J Hydrophobic interactions: H:W.38, H:W.38, D:V.11, D:V.59 Hydrogen bonds: H:Y.5, J:R.45, J:Q.57, J:Q.57 Water bridges: H:D.37, D:Q.57 Salt bridges: H:K.3 pi-Stacking: H:W.38, H:W.38, H:W.38 FMN.29: 14 residues within 4Å: Chain E: V.11, R.45, Q.57, V.59 Chain I: K.3, Y.5, D.37, W.38, A.65 Chain L: R.45, T.47, Q.57 Ligands: FMN.12, NA.28 18 PLIP interactions: 3 interactions with chain L, 12 interactions with chain I, 3 interactions with chain E Hydrogen bonds: L:R.45, L:Q.57, L:Q.57, I:Y.5, I:Y.5 Hydrophobic interactions: I:Y.5, I:W.38, I:W.38, E:V.59 Water bridges: I:K.3, I:H.35, I:D.37, E:Q.57, E:Q.57 Salt bridges: I:K.3 pi-Stacking: I:W.38, I:W.38, I:W.38 FMN.31: 12 residues within 4Å: Chain F: V.11, R.45, Q.57 Chain J: K.3, Y.5, D.37, W.38, A.65 Chain K: R.45, T.47, Q.57 Ligands: FMN.10 18 PLIP interactions: 3 interactions with chain K, 13 interactions with chain J, 2 interactions with chain F Hydrogen bonds: K:R.45, K:Q.57, K:Q.57, J:Y.5 Hydrophobic interactions: J:Y.5, J:W.38, J:W.38, F:V.11 Water bridges: J:K.3, J:K.3, J:Y.5, J:D.37, J:D.37, F:Q.57 Salt bridges: J:K.3 pi-Stacking: J:W.38, J:W.38, J:W.38 FMN.33: 13 residues within 4Å: Chain G: V.11, R.45, Q.57, V.59 Chain H: R.45, T.47, Q.57 Chain K: K.3, Y.5, D.37, W.38, A.65 Ligands: FMN.34 17 PLIP interactions: 2 interactions with chain G, 12 interactions with chain K, 3 interactions with chain H Hydrophobic interactions: G:V.59, K:Y.5, K:W.38, K:W.38 Water bridges: G:Q.57, K:K.3, K:Y.5, K:D.37, K:D.37 Hydrogen bonds: K:Y.5, H:R.45, H:Q.57, H:Q.57 Salt bridges: K:K.3 pi-Stacking: K:W.38, K:W.38, K:W.38 FMN.34: 14 residues within 4Å: Chain G: R.45, T.47, Q.57 Chain H: V.11, R.45, Q.57, V.59 Chain L: K.3, Y.5, D.37, W.38, A.65 Ligands: FMN.33, NA.36 14 PLIP interactions: 9 interactions with chain L, 3 interactions with chain G, 2 interactions with chain H Hydrophobic interactions: L:W.38, L:W.38, H:V.59 Hydrogen bonds: L:Y.5, L:Y.5, G:R.45, G:Q.57, G:Q.57 Water bridges: L:K.3, H:Q.57 Salt bridges: L:K.3 pi-Stacking: L:W.38, L:W.38, L:W.38

12 x COA: COENZYME A(Non-covalent)

COA.3: 21 residues within 4Å: Chain A: R.28, T.32, L.33, R.34, H.35, F.64, A.65, L.66, E.67 Chain E: K.6, V.8, L.10, R.28, A.29, L.33, F.64, L.66 Chain I: K.6, L.66 Ligands: COA.16, COA.30 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain E Hydrogen bonds: A:T.32, A:T.32, A:R.34, A:R.34, A:R.34, A:A.65, A:E.67, E:K.6 Salt bridges: A:R.28 pi-Cation interactions: A:R.34 Hydrophobic interactions: E:L.33, E:L.66 COA.6: 22 residues within 4Å: Chain B: R.28, T.32, L.33, R.34, H.35, F.64, A.65, L.66, E.67 Chain F: K.6, V.8, L.10, R.28, A.29, T.32, L.33, F.64, L.66 Chain J: K.6, L.66 Ligands: COA.19, COA.32 14 PLIP interactions: 3 interactions with chain F, 11 interactions with chain B Hydrophobic interactions: F:L.33, F:L.66 Hydrogen bonds: F:K.6, B:T.32, B:T.32, B:T.32, B:R.34, B:R.34, B:R.34, B:A.65, B:E.67 Water bridges: B:R.28 Salt bridges: B:R.28 pi-Cation interactions: B:R.34 COA.11: 21 residues within 4Å: Chain C: R.28, T.32, L.33, R.34, H.35, F.64, A.65, L.66, E.67 Chain G: K.6, V.8, L.10, R.28, A.29, L.33, F.64, L.66 Chain K: K.6, L.66 Ligands: COA.22, COA.35 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain G Hydrogen bonds: C:T.32, C:T.32, C:R.34, C:R.34, C:R.34, C:A.65, C:E.67, C:E.67, G:K.6 Water bridges: C:R.28, C:R.28 Salt bridges: C:R.28 pi-Cation interactions: C:R.34 Hydrophobic interactions: G:L.66 COA.13: 21 residues within 4Å: Chain D: R.28, T.32, L.33, R.34, H.35, F.64, A.65, L.66, E.67 Chain H: K.6, V.8, L.10, R.28, A.29, L.33, F.64, L.66 Chain L: K.6, L.66 Ligands: COA.25, COA.38 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain H Hydrogen bonds: D:T.32, D:R.34, D:R.34, D:R.34, D:A.65, D:E.67, H:K.6 Salt bridges: D:R.28 pi-Cation interactions: D:R.34 Hydrophobic interactions: H:L.33, H:L.66 COA.16: 19 residues within 4Å: Chain A: K.6, L.66 Chain E: T.32, L.33, R.34, H.35, F.64, A.65, L.66, E.67 Chain I: K.6, V.8, L.10, R.28, A.29, L.33, L.66 Ligands: COA.3, COA.30 11 PLIP interactions: 8 interactions with chain E, 3 interactions with chain I Hydrogen bonds: E:T.32, E:T.32, E:R.34, E:R.34, E:A.65, E:E.67, E:E.67, I:K.6 pi-Cation interactions: E:R.34 Hydrophobic interactions: I:K.6, I:L.66 COA.19: 21 residues within 4Å: Chain B: K.6, L.66 Chain F: R.28, T.32, L.33, R.34, H.35, F.64, A.65, L.66, E.67 Chain J: K.6, V.8, L.10, R.28, A.29, L.33, F.64, L.66 Ligands: COA.6, COA.32 13 PLIP interactions: 10 interactions with chain F, 3 interactions with chain J Hydrogen bonds: F:T.32, F:R.34, F:R.34, F:R.34, F:A.65, F:E.67, F:E.67, J:K.6 Water bridges: F:R.28 Salt bridges: F:R.28 pi-Cation interactions: F:R.34 Hydrophobic interactions: J:L.33, J:L.66 COA.22: 21 residues within 4Å: Chain C: K.6, L.66 Chain G: R.28, T.32, L.33, R.34, H.35, F.64, A.65, L.66, E.67 Chain K: K.6, V.8, L.10, R.28, A.29, L.33, F.64, L.66 Ligands: COA.11, COA.35 12 PLIP interactions: 9 interactions with chain G, 3 interactions with chain K Hydrogen bonds: G:T.32, G:R.34, G:R.34, G:R.34, G:A.65, G:E.67, G:E.67, K:K.6 Salt bridges: G:R.28 pi-Cation interactions: G:R.34 Hydrophobic interactions: K:L.33, K:L.66 COA.25: 22 residues within 4Å: Chain D: K.6, L.66 Chain H: R.28, T.32, L.33, R.34, H.35, F.64, A.65, L.66, E.67 Chain L: K.6, V.8, L.10, R.28, A.29, T.32, L.33, F.64, L.66 Ligands: COA.13, COA.38 13 PLIP interactions: 10 interactions with chain H, 3 interactions with chain L Hydrogen bonds: H:T.32, H:T.32, H:R.34, H:R.34, H:R.34, H:A.65, H:E.67, L:K.6 Water bridges: H:R.28 Salt bridges: H:R.28 pi-Cation interactions: H:R.34 Hydrophobic interactions: L:L.33, L:L.66 COA.30: 21 residues within 4Å: Chain A: K.6, V.8, L.10, R.28, A.29, L.33, F.64, L.66 Chain E: K.6, L.66 Chain I: R.28, T.32, L.33, R.34, H.35, F.64, A.65, L.66, E.67 Ligands: COA.3, COA.16 12 PLIP interactions: 10 interactions with chain I, 2 interactions with chain A Hydrogen bonds: I:T.32, I:R.34, I:R.34, I:R.34, I:A.65, I:E.67, A:K.6 Water bridges: I:R.28, I:R.28 Salt bridges: I:R.28 pi-Cation interactions: I:R.34 Hydrophobic interactions: A:L.66 COA.32: 21 residues within 4Å: Chain B: K.6, V.8, L.10, R.28, A.29, L.33, F.64, L.66 Chain F: K.6, L.66 Chain J: R.28, T.32, L.33, R.34, H.35, F.64, A.65, L.66, E.67 Ligands: COA.6, COA.19 12 PLIP interactions: 3 interactions with chain B, 9 interactions with chain J Hydrophobic interactions: B:L.33, B:L.66 Hydrogen bonds: B:K.6, J:T.32, J:T.32, J:R.34, J:R.34, J:R.34, J:A.65, J:E.67 Salt bridges: J:R.28 pi-Cation interactions: J:R.34 COA.35: 19 residues within 4Å: Chain C: K.6, V.8, L.10, R.28, A.29, L.33, L.66 Chain G: K.6, L.66 Chain K: T.32, L.33, R.34, H.35, F.64, A.65, L.66, E.67 Ligands: COA.11, COA.22 9 PLIP interactions: 6 interactions with chain K, 3 interactions with chain C Hydrogen bonds: K:T.32, K:R.34, K:R.34, K:A.65, K:E.67, C:K.6 pi-Cation interactions: K:R.34 Hydrophobic interactions: C:K.6, C:L.66 COA.38: 21 residues within 4Å: Chain D: K.6, V.8, L.10, R.28, A.29, L.33, F.64, L.66 Chain H: K.6, L.66 Chain L: R.28, T.32, L.33, R.34, H.35, F.64, A.65, L.66, E.67 Ligands: COA.13, COA.25 13 PLIP interactions: 10 interactions with chain L, 3 interactions with chain D Hydrogen bonds: L:T.32, L:T.32, L:R.34, L:R.34, L:R.34, L:A.65, L:E.67, D:K.6 Water bridges: L:R.28 Salt bridges: L:R.28 pi-Cation interactions: L:R.34 Hydrophobic interactions: D:L.33, D:L.66

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 6 residues within 4Å: Chain B: E.9, K.42, E.43, V.59 Chain F: K.7, K.42 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain B Salt bridges: F:K.7, F:K.42 Hydrogen bonds: B:E.9, B:E.43 PO4.7: 6 residues within 4Å: Chain C: E.9, K.42, E.43, V.59 Chain G: K.7, K.42 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain G Hydrogen bonds: C:E.9, C:E.43 Salt bridges: C:K.42, G:K.7, G:K.42 Water bridges: G:K.42 PO4.18: 6 residues within 4Å: Chain F: E.9, K.42, E.43, V.59 Chain J: K.7, K.42 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain F Water bridges: J:K.42 Salt bridges: J:K.7, J:K.42 Hydrogen bonds: F:E.43 PO4.23: 6 residues within 4Å: Chain H: E.9, K.42, E.43, V.59 Chain L: K.7, K.42 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain H Salt bridges: L:K.7, L:K.42 Hydrogen bonds: H:E.9 PO4.26: 6 residues within 4Å: Chain A: K.7, K.42 Chain I: E.9, K.42, E.43, V.59 5 PLIP interactions: 2 interactions with chain I, 3 interactions with chain A Hydrogen bonds: I:E.9 Salt bridges: I:K.42, A:K.7, A:K.42 Water bridges: A:K.42 PO4.37: 6 residues within 4Å: Chain D: K.7, K.42 Chain L: E.9, K.42, E.43, V.59 5 PLIP interactions: 2 interactions with chain L, 3 interactions with chain D Hydrogen bonds: L:E.43, L:E.43 Water bridges: D:K.42 Salt bridges: D:K.7, D:K.42

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
A

H
B

I
C

J
D

K
E

L
F

DODECIN