SMTL ID : 2yiz.1

X-ray structure of Mycobacterium tuberculosis Dodecin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-12-mer

Ligands

12 x COA: COENZYME A(Non-covalent)

COA.1: 5 residues within 4Å: Chain A: R.34, F.64, R.65, L.66, E.67 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.34, A:R.34, A:E.67 pi-Cation interactions: A:R.34 COA.6: 6 residues within 4Å: Chain B: T.32, R.34, F.64, R.65, L.66, E.67 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.34, B:R.34, B:R.34, B:E.67 pi-Cation interactions: B:R.34 COA.11: 5 residues within 4Å: Chain C: R.34, F.64, R.65, L.66, E.67 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.34, C:R.34, C:E.67 pi-Cation interactions: C:R.34 COA.15: 6 residues within 4Å: Chain D: T.32, R.34, F.64, R.65, L.66, E.67 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.34, D:R.34, D:R.34, D:E.67 pi-Cation interactions: D:R.34 COA.17: 5 residues within 4Å: Chain E: R.34, F.64, R.65, L.66, E.67 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.34, E:R.34, E:E.67 pi-Cation interactions: E:R.34 COA.22: 6 residues within 4Å: Chain F: T.32, R.34, F.64, R.65, L.66, E.67 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:R.34, F:R.34, F:R.34, F:E.67 pi-Cation interactions: F:R.34 COA.27: 5 residues within 4Å: Chain G: R.34, F.64, R.65, L.66, E.67 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:R.34, G:R.34, G:E.67 pi-Cation interactions: G:R.34 COA.31: 6 residues within 4Å: Chain H: T.32, R.34, F.64, R.65, L.66, E.67 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:R.34, H:R.34, H:R.34, H:E.67 pi-Cation interactions: H:R.34 COA.33: 5 residues within 4Å: Chain I: R.34, F.64, R.65, L.66, E.67 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:R.34, I:R.34, I:E.67 pi-Cation interactions: I:R.34 COA.38: 6 residues within 4Å: Chain J: T.32, R.34, F.64, R.65, L.66, E.67 5 PLIP interactions: 5 interactions with chain J Hydrogen bonds: J:R.34, J:R.34, J:R.34, J:E.67 pi-Cation interactions: J:R.34 COA.43: 5 residues within 4Å: Chain K: R.34, F.64, R.65, L.66, E.67 4 PLIP interactions: 4 interactions with chain K Hydrogen bonds: K:R.34, K:R.34, K:E.67 pi-Cation interactions: K:R.34 COA.47: 6 residues within 4Å: Chain L: T.32, R.34, F.64, R.65, L.66, E.67 5 PLIP interactions: 5 interactions with chain L Hydrogen bonds: L:R.34, L:R.34, L:R.34, L:E.67 pi-Cation interactions: L:R.34

12 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 12 residues within 4Å: Chain A: H.3, Y.5, D.37, W.38, R.65 Chain C: V.11, Q.57, T.59 Chain D: R.45, H.47, Q.57 Ligands: FMN.44 11 PLIP interactions: 7 interactions with chain A, 1 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: A:W.38, C:Q.57 Hydrogen bonds: A:D.37, D:R.45, D:Q.57, D:Q.57 Salt bridges: A:H.3, A:R.65 pi-Stacking: A:W.38, A:W.38, A:W.38 FMN.7: 12 residues within 4Å: Chain A: R.45, H.47, Q.57 Chain B: H.3, Y.5, D.37, W.38, R.65 Chain F: V.11, Q.57, T.59 Ligands: FMN.32 11 PLIP interactions: 6 interactions with chain B, 1 interactions with chain F, 4 interactions with chain A Hydrophobic interactions: B:W.38, F:Q.57 Hydrogen bonds: B:D.37, A:R.45, A:H.47, A:Q.57, A:Q.57 Salt bridges: B:H.3, B:R.65 pi-Stacking: B:W.38, B:W.38 FMN.12: 12 residues within 4Å: Chain C: H.3, Y.5, D.37, W.38, R.65 Chain G: R.45, H.47, Q.57 Chain H: V.11, Q.57, T.59 Ligands: FMN.18 12 PLIP interactions: 4 interactions with chain G, 7 interactions with chain C, 1 interactions with chain H Hydrogen bonds: G:R.45, G:H.47, G:Q.57, G:Q.57, C:Y.5, C:D.37 Hydrophobic interactions: C:W.38, H:Q.57 Salt bridges: C:H.3, C:R.65 pi-Stacking: C:W.38, C:W.38 FMN.16: 12 residues within 4Å: Chain B: R.45, H.47, Q.57 Chain D: H.3, Y.5, D.37, W.38, R.65 Chain I: V.11, Q.57, T.59 Ligands: FMN.39 11 PLIP interactions: 3 interactions with chain B, 7 interactions with chain D, 1 interactions with chain I Hydrogen bonds: B:R.45, B:Q.57, B:Q.57, D:Y.5, D:D.37 Hydrophobic interactions: D:W.38, I:Q.57 Salt bridges: D:H.3, D:R.65 pi-Stacking: D:W.38, D:W.38 FMN.18: 12 residues within 4Å: Chain E: H.3, Y.5, D.37, W.38, R.65 Chain G: V.11, Q.57, T.59 Chain H: R.45, H.47, Q.57 Ligands: FMN.12 11 PLIP interactions: 7 interactions with chain E, 3 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: E:W.38, G:Q.57 Hydrogen bonds: E:D.37, H:R.45, H:Q.57, H:Q.57 Salt bridges: E:H.3, E:R.65 pi-Stacking: E:W.38, E:W.38, E:W.38 FMN.23: 12 residues within 4Å: Chain E: R.45, H.47, Q.57 Chain F: H.3, Y.5, D.37, W.38, R.65 Chain J: V.11, Q.57, T.59 Ligands: FMN.48 11 PLIP interactions: 1 interactions with chain J, 4 interactions with chain E, 6 interactions with chain F Hydrophobic interactions: J:Q.57, F:W.38 Hydrogen bonds: E:R.45, E:H.47, E:Q.57, E:Q.57, F:D.37 Salt bridges: F:H.3, F:R.65 pi-Stacking: F:W.38, F:W.38 FMN.28: 12 residues within 4Å: Chain G: H.3, Y.5, D.37, W.38, R.65 Chain K: R.45, H.47, Q.57 Chain L: V.11, Q.57, T.59 Ligands: FMN.34 12 PLIP interactions: 4 interactions with chain K, 7 interactions with chain G, 1 interactions with chain L Hydrogen bonds: K:R.45, K:H.47, K:Q.57, K:Q.57, G:Y.5, G:D.37 Hydrophobic interactions: G:W.38, L:Q.57 Salt bridges: G:H.3, G:R.65 pi-Stacking: G:W.38, G:W.38 FMN.32: 12 residues within 4Å: Chain A: V.11, Q.57, T.59 Chain F: R.45, H.47, Q.57 Chain H: H.3, Y.5, D.37, W.38, R.65 Ligands: FMN.7 11 PLIP interactions: 7 interactions with chain H, 3 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: H:W.38, A:Q.57 Hydrogen bonds: H:Y.5, H:D.37, F:R.45, F:Q.57, F:Q.57 Salt bridges: H:H.3, H:R.65 pi-Stacking: H:W.38, H:W.38 FMN.34: 12 residues within 4Å: Chain I: H.3, Y.5, D.37, W.38, R.65 Chain K: V.11, Q.57, T.59 Chain L: R.45, H.47, Q.57 Ligands: FMN.28 11 PLIP interactions: 7 interactions with chain I, 3 interactions with chain L, 1 interactions with chain K Hydrophobic interactions: I:W.38, K:Q.57 Hydrogen bonds: I:D.37, L:R.45, L:Q.57, L:Q.57 Salt bridges: I:H.3, I:R.65 pi-Stacking: I:W.38, I:W.38, I:W.38 FMN.39: 12 residues within 4Å: Chain B: V.11, Q.57, T.59 Chain I: R.45, H.47, Q.57 Chain J: H.3, Y.5, D.37, W.38, R.65 Ligands: FMN.16 11 PLIP interactions: 6 interactions with chain J, 1 interactions with chain B, 4 interactions with chain I Hydrophobic interactions: J:W.38, B:Q.57 Hydrogen bonds: J:D.37, I:R.45, I:H.47, I:Q.57, I:Q.57 Salt bridges: J:H.3, J:R.65 pi-Stacking: J:W.38, J:W.38 FMN.44: 12 residues within 4Å: Chain C: R.45, H.47, Q.57 Chain D: V.11, Q.57, T.59 Chain K: H.3, Y.5, D.37, W.38, R.65 Ligands: FMN.2 12 PLIP interactions: 4 interactions with chain C, 7 interactions with chain K, 1 interactions with chain D Hydrogen bonds: C:R.45, C:H.47, C:Q.57, C:Q.57, K:Y.5, K:D.37 Hydrophobic interactions: K:W.38, D:Q.57 Salt bridges: K:H.3, K:R.65 pi-Stacking: K:W.38, K:W.38 FMN.48: 12 residues within 4Å: Chain E: V.11, Q.57, T.59 Chain J: R.45, H.47, Q.57 Chain L: H.3, Y.5, D.37, W.38, R.65 Ligands: FMN.23 11 PLIP interactions: 7 interactions with chain L, 3 interactions with chain J, 1 interactions with chain E Hydrophobic interactions: L:W.38, E:Q.57 Hydrogen bonds: L:Y.5, L:D.37, J:R.45, J:Q.57, J:Q.57 Salt bridges: L:H.3, L:R.65 pi-Stacking: L:W.38, L:W.38

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: V.7, E.9 Chain C: V.7, I.8, E.9, K.61 Chain H: V.7, I.8, E.9, K.61 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain H Hydrogen bonds: C:V.7, C:E.9, C:E.9, H:V.7 Water bridges: C:E.9 GOL.4: 3 residues within 4Å: Chain A: R.6 Chain C: R.6 Chain H: R.6 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain H, 2 interactions with chain C Hydrogen bonds: A:R.6, A:R.6, H:R.6, H:R.6, C:R.6, C:R.6 GOL.5: 4 residues within 4Å: Chain A: V.41 Chain B: Q.42, I.44 Chain D: V.41 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.41, B:Q.42 Water bridges: A:V.41 GOL.8: 6 residues within 4Å: Chain A: V.18, D.19 Chain B: V.18, D.19 Chain D: V.18, D.19 12 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B, 3 interactions with chain D Hydrogen bonds: A:V.18, A:D.19, B:V.18, B:D.19, B:D.19, D:V.18, D:D.19 Water bridges: A:G.17, A:D.19, A:A.20, B:A.20, D:A.20 GOL.9: 15 residues within 4Å: Chain B: V.7, I.8, E.9, K.61 Chain F: V.7, I.8, E.9, K.61 Chain J: V.7, I.8, E.9 Ligands: GOL.25, CL.26, GOL.41, CL.42 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:I.8, B:E.9, F:I.8 Water bridges: B:E.9 GOL.19: 10 residues within 4Å: Chain E: V.7, E.9 Chain G: V.7, I.8, E.9, K.61 Chain L: V.7, I.8, E.9, K.61 5 PLIP interactions: 1 interactions with chain L, 4 interactions with chain G Hydrogen bonds: L:V.7, G:V.7, G:E.9, G:E.9 Water bridges: G:E.9 GOL.20: 3 residues within 4Å: Chain E: R.6 Chain G: R.6 Chain L: R.6 6 PLIP interactions: 2 interactions with chain G, 2 interactions with chain E, 2 interactions with chain L Hydrogen bonds: G:R.6, G:R.6, E:R.6, E:R.6, L:R.6, L:R.6 GOL.21: 4 residues within 4Å: Chain E: V.41 Chain F: Q.42, I.44 Chain H: V.41 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:V.41, F:Q.42 Water bridges: E:V.41 GOL.24: 6 residues within 4Å: Chain E: V.18, D.19 Chain F: V.18, D.19 Chain H: V.18, D.19 12 PLIP interactions: 4 interactions with chain F, 3 interactions with chain H, 5 interactions with chain E Hydrogen bonds: F:V.18, F:D.19, F:D.19, H:V.18, H:D.19, E:V.18, E:D.19 Water bridges: F:A.20, H:A.20, E:G.17, E:D.19, E:A.20 GOL.25: 15 residues within 4Å: Chain B: V.7, I.8, E.9 Chain F: V.7, I.8, E.9, K.61 Chain J: V.7, I.8, E.9, K.61 Ligands: GOL.9, CL.10, GOL.41, CL.42 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain J Hydrogen bonds: F:I.8, F:E.9, J:I.8 Water bridges: F:E.9 GOL.35: 10 residues within 4Å: Chain D: V.7, I.8, E.9, K.61 Chain I: V.7, E.9 Chain K: V.7, I.8, E.9, K.61 5 PLIP interactions: 4 interactions with chain K, 1 interactions with chain D Hydrogen bonds: K:V.7, K:E.9, K:E.9, D:V.7 Water bridges: K:E.9 GOL.36: 3 residues within 4Å: Chain D: R.6 Chain I: R.6 Chain K: R.6 6 PLIP interactions: 2 interactions with chain I, 2 interactions with chain K, 2 interactions with chain D Hydrogen bonds: I:R.6, I:R.6, K:R.6, K:R.6, D:R.6, D:R.6 GOL.37: 4 residues within 4Å: Chain I: V.41 Chain J: Q.42, I.44 Chain L: V.41 3 PLIP interactions: 1 interactions with chain J, 2 interactions with chain I Hydrogen bonds: J:Q.42, I:V.41 Water bridges: I:V.41 GOL.40: 6 residues within 4Å: Chain I: V.18, D.19 Chain J: V.18, D.19 Chain L: V.18, D.19 12 PLIP interactions: 3 interactions with chain L, 4 interactions with chain J, 5 interactions with chain I Hydrogen bonds: L:V.18, L:D.19, J:V.18, J:D.19, J:D.19, I:V.18, I:D.19 Water bridges: L:A.20, J:A.20, I:G.17, I:D.19, I:A.20 GOL.41: 15 residues within 4Å: Chain B: V.7, I.8, E.9, K.61 Chain F: V.7, I.8, E.9 Chain J: V.7, I.8, E.9, K.61 Ligands: GOL.9, CL.10, GOL.25, CL.26 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain J Hydrogen bonds: B:I.8, J:I.8, J:E.9 Water bridges: J:E.9

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

CL.10: 8 residues within 4Å: Chain B: R.6, I.8 Chain F: R.6 Chain J: R.6 Ligands: GOL.25, CL.26, GOL.41, CL.42 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: R.6 Chain C: R.6 Chain H: R.6 Ligand excluded by PLIP CL.26: 8 residues within 4Å: Chain B: R.6 Chain F: R.6, I.8 Chain J: R.6 Ligands: GOL.9, CL.10, GOL.41, CL.42 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain E: R.6 Chain G: R.6 Chain L: R.6 Ligand excluded by PLIP CL.42: 8 residues within 4Å: Chain B: R.6 Chain F: R.6 Chain J: R.6, I.8 Ligands: GOL.9, CL.10, GOL.25, CL.26 Ligand excluded by PLIP CL.46: 3 residues within 4Å: Chain D: R.6 Chain I: R.6 Chain K: R.6 Ligand excluded by PLIP

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.13: 11 residues within 4Å: Chain C: G.17, V.18, D.19 Chain G: G.17, V.18, D.19 Chain K: G.17, V.18, D.19 Ligands: TRS.29, TRS.45 13 PLIP interactions: 5 interactions with chain C, 5 interactions with chain G, 3 interactions with chain K Hydrogen bonds: C:V.18, C:D.19, G:V.18, G:D.19, G:D.19, K:V.18, K:D.19 Water bridges: C:G.17, C:D.19, C:A.20, G:D.19, G:A.20, K:A.20 TRS.29: 11 residues within 4Å: Chain C: G.17, V.18, D.19 Chain G: G.17, V.18, D.19 Chain K: G.17, V.18, D.19 Ligands: TRS.13, TRS.45 13 PLIP interactions: 5 interactions with chain C, 4 interactions with chain K, 4 interactions with chain G Hydrogen bonds: C:V.18, C:D.19, K:V.18, K:D.19, K:D.19, G:V.18, G:D.19 Water bridges: C:G.17, C:D.19, C:A.20, K:A.20, G:D.19, G:A.20 TRS.45: 11 residues within 4Å: Chain C: G.17, V.18, D.19 Chain G: G.17, V.18, D.19 Chain K: G.17, V.18, D.19 Ligands: TRS.13, TRS.29 13 PLIP interactions: 4 interactions with chain G, 3 interactions with chain K, 6 interactions with chain C Hydrogen bonds: G:V.18, G:D.19, K:V.18, K:D.19, C:V.18, C:D.19, C:D.19 Water bridges: G:D.19, G:A.20, K:A.20, C:G.17, C:D.19, C:A.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vinzenz, X. et al., Chemical Engineering of Mycobacterium Tuberculosis Dodecin Hybrids. Chem.Commun.(Camb.) (2011)

Release Date

2011-10-12

Peptides

DODECIN: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

DODECIN