SMTL ID : 2v21.1

Crystal structure of the T. thermophilus dodecin in complex with prebound FMN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-12-mer

Ligands

6 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 11 residues within 4Å: Chain A: K.3, Y.5, D.37, W.38, R.65 Chain B: R.45, T.47, Q.57 Chain K: V.11, R.45, Q.57 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.5, A:W.38 Hydrogen bonds: A:Y.5, B:R.45, B:Q.57, B:Q.57 Salt bridges: A:R.65 pi-Stacking: A:W.38, A:W.38, A:W.38 FMN.3: 12 residues within 4Å: Chain A: R.45, T.47, Q.57 Chain C: K.3, Y.5, D.37, W.38, R.65 Chain G: V.11, R.45, Q.57 Ligands: FMN.8 11 PLIP interactions: 1 interactions with chain G, 7 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: G:R.45, C:Y.5, C:W.38 Hydrogen bonds: C:Y.5, A:R.45, A:Q.57, A:Q.57 Salt bridges: C:R.65 pi-Stacking: C:W.38, C:W.38, C:W.38 FMN.4: 13 residues within 4Å: Chain D: R.45, T.47, Q.57 Chain F: K.3, Y.5, D.37, W.38, R.65 Chain J: V.11, R.45, Q.57, V.59 Ligands: FMN.9 12 PLIP interactions: 3 interactions with chain D, 8 interactions with chain F, 1 interactions with chain J Hydrogen bonds: D:R.45, D:Q.57, D:Q.57, F:Y.5 Hydrophobic interactions: F:Y.5, F:W.38, F:W.38, J:V.59 Salt bridges: F:R.65 pi-Stacking: F:W.38, F:W.38, F:W.38 FMN.6: 11 residues within 4Å: Chain E: V.11, R.45, Q.57 Chain G: K.3, Y.5, D.37, W.38, R.65 Chain H: R.45, T.47, Q.57 11 PLIP interactions: 8 interactions with chain G, 3 interactions with chain H Hydrophobic interactions: G:Y.5, G:W.38 Hydrogen bonds: G:Y.5, G:Y.5, H:R.45, H:Q.57, H:Q.57 Salt bridges: G:R.65 pi-Stacking: G:W.38, G:W.38, G:W.38 FMN.8: 12 residues within 4Å: Chain A: V.11, R.45, Q.57 Chain G: R.45, T.47, Q.57 Chain I: K.3, Y.5, D.37, W.38, R.65 Ligands: FMN.3 12 PLIP interactions: 3 interactions with chain G, 1 interactions with chain A, 8 interactions with chain I Hydrogen bonds: G:R.45, G:Q.57, G:Q.57, I:Y.5, I:Y.5 Hydrophobic interactions: A:R.45, I:Y.5, I:W.38 Salt bridges: I:R.65 pi-Stacking: I:W.38, I:W.38, I:W.38 FMN.9: 13 residues within 4Å: Chain D: V.11, R.45, Q.57, V.59 Chain J: R.45, T.47, Q.57 Chain L: K.3, Y.5, D.37, W.38, R.65 Ligands: FMN.4 13 PLIP interactions: 3 interactions with chain J, 9 interactions with chain L, 1 interactions with chain D Hydrogen bonds: J:R.45, J:Q.57, J:Q.57, L:Y.5, L:Y.5 Hydrophobic interactions: L:Y.5, L:W.38, L:W.38, D:V.59 Salt bridges: L:R.65 pi-Stacking: L:W.38, L:W.38, L:W.38

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

NA.2: 3 residues within 4Å: Chain A: E.19 Chain B: E.19 Chain C: E.19 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.19 NA.5: 4 residues within 4Å: Chain D: E.19 Chain E: E.19 Chain F: L.18, E.19 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.19 NA.7: 3 residues within 4Å: Chain G: E.19 Chain H: E.19 Chain I: E.19 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:E.19 NA.10: 4 residues within 4Å: Chain J: E.19 Chain K: E.19 Chain L: L.18, E.19 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:E.19

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

HYPOTHETICAL PROTEIN TTHA1431: 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

HYPOTHETICAL PROTEIN TTHA1431

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