SMTL ID : 2vyx.1

Crystal structure of the T. thermophilus dodecin W38F mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-12-mer

Ligands

12 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 12 residues within 4Å: Chain A: K.3, Y.5, D.37, F.38, R.65 Chain B: R.45, T.47, Q.57 Chain H: V.11, R.45, Q.57 Ligands: FMN.3 11 PLIP interactions: 1 interactions with chain H, 7 interactions with chain A, 3 interactions with chain B Water bridges: H:Q.57, A:D.37 Hydrophobic interactions: A:Y.5, A:F.38 Hydrogen bonds: A:Y.5, A:D.37, B:R.45, B:Q.57, B:Q.57 Salt bridges: A:R.65 pi-Stacking: A:F.38 FMN.3: 12 residues within 4Å: Chain B: V.11, R.45, Q.57 Chain G: K.3, Y.5, D.37, F.38, R.65 Chain H: R.45, T.47, Q.57 Ligands: FMN.1 13 PLIP interactions: 3 interactions with chain H, 8 interactions with chain G, 2 interactions with chain B Hydrogen bonds: H:R.45, H:Q.57, H:Q.57, G:D.37 Hydrophobic interactions: G:Y.5, G:F.38, B:V.11 Water bridges: G:D.37, B:Q.57 Salt bridges: G:K.3, G:R.65 pi-Stacking: G:F.38, G:F.38 FMN.6: 12 residues within 4Å: Chain B: K.3, Y.5, D.37, F.38, R.65 Chain C: R.45, T.47, Q.57 Chain F: V.11, R.45, Q.57 Ligands: FMN.8 10 PLIP interactions: 4 interactions with chain B, 4 interactions with chain C, 2 interactions with chain F Hydrogen bonds: B:Y.5, B:Y.5, C:R.45, C:Q.57, C:Q.57 Salt bridges: B:R.65 pi-Stacking: B:F.38 Water bridges: C:I.48, F:Q.57, F:Q.57 FMN.8: 12 residues within 4Å: Chain C: V.11, Q.57, V.59 Chain E: K.3, Y.5, D.37, F.38, R.65 Chain F: R.45, T.47, Q.57 Ligands: FMN.6 11 PLIP interactions: 3 interactions with chain F, 2 interactions with chain C, 6 interactions with chain E Hydrogen bonds: F:R.45, F:Q.57, F:Q.57, E:D.37 Hydrophobic interactions: C:V.59, E:Y.5 Water bridges: C:Q.57, E:D.37, E:D.37 Salt bridges: E:R.65 pi-Stacking: E:F.38 FMN.10: 12 residues within 4Å: Chain A: R.45, T.47, Q.57 Chain C: K.3, Y.5, D.37, F.38, R.65 Chain J: V.11, R.45, Q.57 Ligands: FMN.12 13 PLIP interactions: 9 interactions with chain C, 3 interactions with chain A, 1 interactions with chain J Hydrophobic interactions: C:Y.5, C:F.38 Hydrogen bonds: C:D.37, A:R.45, A:Q.57, A:Q.57 Water bridges: C:D.37, C:R.65, C:R.65, J:Q.57 Salt bridges: C:R.65 pi-Stacking: C:F.38, C:F.38 FMN.12: 11 residues within 4Å: Chain A: V.11, Q.57 Chain J: R.45, T.47, Q.57 Chain L: K.3, Y.5, D.37, F.38, R.65 Ligands: FMN.10 15 PLIP interactions: 10 interactions with chain L, 2 interactions with chain A, 3 interactions with chain J Hydrogen bonds: L:Y.5, L:D.37, J:R.45, J:Q.57, J:Q.57 Water bridges: L:K.3, L:K.3, L:R.65, L:R.65, A:Q.57 Salt bridges: L:K.3, L:R.65 pi-Stacking: L:F.38, L:F.38 Hydrophobic interactions: A:V.11 FMN.14: 12 residues within 4Å: Chain D: K.3, Y.5, D.37, F.38, R.65 Chain E: R.45, T.47, Q.57 Chain K: V.11, R.45, Q.57 Ligands: FMN.16 16 PLIP interactions: 2 interactions with chain K, 11 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: K:V.11, D:Y.5, D:F.38 Water bridges: K:Q.57, D:Y.5, D:D.37, D:D.37, D:E.40 Hydrogen bonds: D:Y.5, E:R.45, E:Q.57, E:Q.57 Salt bridges: D:K.3, D:R.65 pi-Stacking: D:F.38, D:F.38 FMN.16: 11 residues within 4Å: Chain E: V.11, R.45, Q.57 Chain J: Y.5, D.37, F.38, R.65 Chain K: R.45, T.47, Q.57 Ligands: FMN.14 12 PLIP interactions: 7 interactions with chain J, 2 interactions with chain E, 3 interactions with chain K Hydrogen bonds: J:Y.5, J:D.37, K:R.45, K:Q.57, K:Q.57 Water bridges: J:R.65, J:R.65, E:Q.57 Salt bridges: J:R.65 pi-Stacking: J:F.38, J:F.38 Hydrophobic interactions: E:V.11 FMN.19: 12 residues within 4Å: Chain D: R.45, T.47, Q.57 Chain F: K.3, Y.5, D.37, F.38, R.65 Chain G: V.11, Q.57 Ligands: FMN.21, NA.22 16 PLIP interactions: 11 interactions with chain F, 2 interactions with chain G, 3 interactions with chain D Hydrophobic interactions: F:F.38, G:V.11 Hydrogen bonds: F:D.37, D:R.45, D:Q.57, D:Q.57 Water bridges: F:K.3, F:K.3, F:D.37, F:D.37, F:E.40, G:Q.57 Salt bridges: F:K.3, F:R.65 pi-Stacking: F:F.38, F:F.38 FMN.21: 12 residues within 4Å: Chain D: V.11, Q.57 Chain G: R.45, T.47, Q.57 Chain I: K.3, Y.5, D.37, F.38, R.65 Ligands: FMN.19, NA.22 14 PLIP interactions: 10 interactions with chain I, 3 interactions with chain G, 1 interactions with chain D Hydrophobic interactions: I:Y.5, I:F.38 Hydrogen bonds: I:Y.5, G:R.45, G:Q.57, G:Q.57 Water bridges: I:D.37, I:E.40, I:R.65, I:R.65, D:Q.57 Salt bridges: I:R.65 pi-Stacking: I:F.38, I:F.38 FMN.24: 12 residues within 4Å: Chain H: K.3, Y.5, D.37, F.38, R.65 Chain I: R.45, T.47, Q.57 Chain L: V.11, R.45, Q.57 Ligands: FMN.25 11 PLIP interactions: 2 interactions with chain L, 3 interactions with chain I, 6 interactions with chain H Hydrophobic interactions: L:V.11, H:Y.5, H:F.38 Water bridges: L:Q.57 Hydrogen bonds: I:R.45, I:Q.57, I:Q.57, H:Y.5, H:Y.5 Salt bridges: H:R.65 pi-Stacking: H:F.38 FMN.25: 12 residues within 4Å: Chain I: V.11, R.45, Q.57 Chain K: K.3, Y.5, D.37, F.38, R.65 Chain L: R.45, T.47, Q.57 Ligands: FMN.24 13 PLIP interactions: 3 interactions with chain L, 8 interactions with chain K, 2 interactions with chain I Hydrogen bonds: L:R.45, L:Q.57, L:Q.57, K:Y.5, K:Y.5 Hydrophobic interactions: K:Y.5, K:F.38, I:V.11 Water bridges: K:R.65, K:R.65, I:Q.57 Salt bridges: K:R.65 pi-Stacking: K:F.38

12 x COA: COENZYME A(Non-covalent)

COA.2: 23 residues within 4Å: Chain A: R.28, T.32, L.33, R.34, H.35, F.64, R.65, L.66, E.67 Chain H: K.6, L.66 Chain L: K.6, V.8, L.10, R.28, A.29, T.32, L.33, F.64, L.66 Ligands: COA.4, CL.5, COA.29 14 PLIP interactions: 1 interactions with chain H, 9 interactions with chain A, 4 interactions with chain L Water bridges: H:R.28 Hydrogen bonds: A:T.32, A:T.32, A:R.34, A:R.34, A:R.34, A:R.34, A:E.67, L:K.6 Salt bridges: A:R.28 pi-Cation interactions: A:R.34 Hydrophobic interactions: L:K.6, L:L.33, L:L.66 COA.4: 22 residues within 4Å: Chain A: K.6, V.8, L.10, R.28, A.29, T.32, L.33, F.64, L.66 Chain H: R.28, T.32, L.33, R.34, H.35, F.64, R.65, L.66, E.67 Chain L: K.6, L.66 Ligands: COA.2, COA.29 11 PLIP interactions: 8 interactions with chain H, 3 interactions with chain A Hydrogen bonds: H:T.32, H:T.32, H:R.34, H:R.34, H:R.65, H:E.67, A:K.6 Salt bridges: H:R.28 pi-Cation interactions: H:R.34 Hydrophobic interactions: A:F.64, A:L.66 COA.7: 21 residues within 4Å: Chain B: R.28, T.32, L.33, R.34, H.35, F.64, R.65, L.66, E.67 Chain F: K.6, L.66 Chain G: K.6, V.8, L.10, R.28, A.29, L.33, F.64, L.66 Ligands: COA.20, COA.23 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain G Hydrogen bonds: B:T.32, B:T.32, B:R.34, B:R.34, B:R.34, B:R.65, B:E.67, G:K.6 Salt bridges: B:R.28 pi-Cation interactions: B:R.34 Hydrophobic interactions: G:L.66 COA.11: 21 residues within 4Å: Chain C: R.28, T.32, L.33, R.34, H.35, F.64, R.65, L.66, E.67 Chain E: K.6, V.8, L.10, R.28, A.29, L.33, F.64, L.66 Chain J: K.6, L.66 Ligands: COA.18, COA.27 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain E Hydrogen bonds: C:T.32, C:R.34, C:R.34, C:R.34, C:R.65, C:E.67, E:K.6 Water bridges: C:R.28, C:E.67 Salt bridges: C:R.28 pi-Cation interactions: C:R.34 Hydrophobic interactions: E:L.33, E:L.66 COA.15: 20 residues within 4Å: Chain D: R.28, T.32, L.33, R.34, F.64, R.65, L.66, E.67 Chain I: K.6, V.8, L.10, R.28, A.29, L.33, F.64, L.66 Chain K: K.6, L.66 Ligands: COA.26, COA.28 12 PLIP interactions: 9 interactions with chain D, 3 interactions with chain I Hydrogen bonds: D:T.32, D:R.34, D:R.34, D:R.34, D:R.65, D:E.67, I:K.6 Water bridges: D:R.28 Salt bridges: D:R.28 pi-Cation interactions: D:R.34 Hydrophobic interactions: I:L.33, I:L.66 COA.18: 21 residues within 4Å: Chain C: K.6, L.66 Chain E: R.28, T.32, L.33, R.34, H.35, F.64, R.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.11, COA.27 15 PLIP interactions: 11 interactions with chain E, 4 interactions with chain J Hydrogen bonds: E:T.32, E:T.32, E:R.34, E:R.34, E:R.34, E:R.65, E:E.67, J:K.6 Water bridges: E:R.28, E:R.28 Salt bridges: E:R.28 pi-Cation interactions: E:R.34 Hydrophobic interactions: J:L.33, J:F.64, J:L.66 COA.20: 22 residues within 4Å: Chain B: K.6, V.8, L.10, R.28, A.29, T.32, L.33, F.64, L.66 Chain F: R.28, T.32, L.33, R.34, H.35, F.64, R.65, L.66, E.67 Chain G: K.6, L.66 Ligands: COA.7, COA.23 12 PLIP interactions: 3 interactions with chain B, 9 interactions with chain F Hydrophobic interactions: B:L.33, B:L.66 Hydrogen bonds: B:K.6, F:T.32, F:R.34, F:R.34, F:R.34, F:R.65, F:E.67 Water bridges: F:R.28 Salt bridges: F:R.28 pi-Cation interactions: F:R.34 COA.23: 21 residues within 4Å: Chain B: K.6, L.66 Chain F: K.6, V.8, L.10, R.28, A.29, L.33, F.64, L.66 Chain G: R.28, T.32, L.33, R.34, H.35, F.64, R.65, L.66, E.67 Ligands: COA.7, COA.20 12 PLIP interactions: 9 interactions with chain G, 3 interactions with chain F Hydrogen bonds: G:T.32, G:R.34, G:R.34, G:R.34, G:R.34, G:E.67, G:E.67, F:K.6 Salt bridges: G:R.28 pi-Cation interactions: G:R.34 Hydrophobic interactions: F:L.33, F:L.66 COA.26: 22 residues within 4Å: Chain D: K.6, L.66 Chain I: R.28, T.32, L.33, R.34, H.35, F.64, R.65, L.66, E.67 Chain K: K.6, V.8, L.10, R.28, A.29, T.32, L.33, F.64, L.66 Ligands: COA.15, COA.28 13 PLIP interactions: 9 interactions with chain I, 4 interactions with chain K Hydrogen bonds: I:T.32, I:T.32, I:R.34, I:R.34, I:R.34, I:R.65, I:E.67, K:K.6 Salt bridges: I:R.28 pi-Cation interactions: I:R.34 Hydrophobic interactions: K:L.33, K:F.64, K:L.66 COA.27: 22 residues within 4Å: Chain C: K.6, V.8, L.10, R.28, A.29, T.32, L.33, F.64, L.66 Chain E: K.6, L.66 Chain J: R.28, T.32, L.33, R.34, H.35, F.64, R.65, L.66, E.67 Ligands: COA.11, COA.18 12 PLIP interactions: 9 interactions with chain J, 3 interactions with chain C Hydrogen bonds: J:T.32, J:T.32, J:R.34, J:R.34, J:R.34, J:R.34, J:E.67, C:K.6 Salt bridges: J:R.28 pi-Cation interactions: J:R.34 Hydrophobic interactions: C:L.33, C:L.66 COA.28: 21 residues within 4Å: Chain D: K.6, V.8, L.10, R.28, A.29, L.33, F.64, L.66 Chain I: K.6, L.66 Chain K: R.28, T.32, L.33, R.34, H.35, F.64, R.65, L.66, E.67 Ligands: COA.15, COA.26 12 PLIP interactions: 9 interactions with chain K, 3 interactions with chain D Hydrogen bonds: K:T.32, K:R.34, K:R.34, K:R.34, K:R.65, K:E.67, D:K.6 Water bridges: K:R.28 Salt bridges: K:R.28 pi-Cation interactions: K:R.34 Hydrophobic interactions: D:L.33, D:L.66 COA.29: 21 residues within 4Å: Chain A: K.6, L.66 Chain H: K.6, V.8, L.10, R.28, A.29, L.33, F.64, L.66 Chain L: R.28, T.32, L.33, R.34, H.35, F.64, R.65, L.66, E.67 Ligands: COA.2, COA.4 13 PLIP interactions: 10 interactions with chain L, 3 interactions with chain H Hydrogen bonds: L:T.32, L:T.32, L:R.34, L:R.34, L:R.34, L:R.65, L:E.67, L:E.67, H:K.6 Salt bridges: L:R.28 pi-Cation interactions: L:R.34 Hydrophobic interactions: H:F.64, H:L.66

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

CL.5: 4 residues within 4Å: Chain A: K.6 Chain H: K.6 Chain L: K.6 Ligands: COA.2 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: K.6 Chain F: K.6 Chain G: K.6 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain C: K.6 Chain E: K.6 Chain J: K.6 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain D: K.6 Chain I: K.6 Chain K: K.6 Ligand excluded by PLIP

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

NA.22: 4 residues within 4Å: Chain D: E.55 Chain I: K.3 Ligands: FMN.19, FMN.21 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain I Water bridges: D:Q.57 Hydrogen bonds: I:K.3, I:K.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gurzadyan, G.G. et al., Ultrafast Charge Transfer Dynamics in Flavoprotein Dodecin. To be Published

Release Date

2009-11-17

Peptides

TTHA1431: 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

TTHA1431