SMTL ID : 2c94.1

LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 3-(1,3,7- TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL) 1,1 difluoropentane-1- PHOSPHATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-pentamer

Ligands

5 x TSF: 3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL) 1,1 DIFLUOROPENTANE-1-PHOSPHATE(Non-covalent)

TSF.1: 22 residues within 4Å: Chain A: S.25, W.27, H.28, G.58, A.59, I.60, E.61, V.81, V.82, I.83, R.84, G.85, Q.86, T.87, H.89, F.90 Chain B: A.113, N.114, R.128, K.138, A.142, A.145 23 PLIP interactions: 5 interactions with chain B, 18 interactions with chain A Hydrogen bonds: B:N.114, B:R.128, B:R.128, B:K.138, A:S.25, A:A.59, A:I.60, A:E.61, A:V.81, A:I.83, A:Q.86, A:T.87, A:T.87 Water bridges: B:N.114, A:W.27, A:W.27, A:H.89, A:F.90 Hydrophobic interactions: A:H.89 pi-Stacking: A:W.27, A:W.27, A:W.27, A:W.27 TSF.6: 20 residues within 4Å: Chain B: S.25, W.27, H.28, G.58, A.59, I.60, E.61, V.81, V.82, I.83, R.84, G.85, Q.86, T.87, H.89 Chain C: A.113, N.114, R.128, K.138, A.145 21 PLIP interactions: 16 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:S.25, B:A.59, B:I.60, B:E.61, B:V.81, B:I.83, B:Q.86, B:T.87, B:T.87, C:N.114, C:R.128, C:R.128, C:K.138 Water bridges: B:E.61, B:V.81, B:V.81, B:F.90, C:I.112 pi-Stacking: B:W.27, B:W.27, B:W.27 TSF.11: 19 residues within 4Å: Chain C: S.25, W.27, H.28, G.58, A.59, I.60, E.61, V.81, V.82, I.83, G.85, Q.86, T.87, H.89 Chain D: A.113, N.114, R.128, K.138, A.145 22 PLIP interactions: 18 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:H.89 Hydrogen bonds: C:S.25, C:A.59, C:I.60, C:E.61, C:V.81, C:I.83, C:G.85, C:Q.86, C:T.87, C:T.87, D:N.114, D:R.128, D:R.128, D:K.138 Water bridges: C:W.27, C:V.81, C:F.90 pi-Stacking: C:W.27, C:W.27, C:W.27, C:W.27 TSF.14: 20 residues within 4Å: Chain D: S.25, W.27, H.28, G.58, A.59, I.60, E.61, V.81, V.82, I.83, R.84, G.85, Q.86, T.87, H.89 Chain E: A.113, N.114, R.128, K.138, A.145 22 PLIP interactions: 16 interactions with chain D, 6 interactions with chain E Hydrogen bonds: D:S.25, D:A.59, D:I.60, D:E.61, D:V.81, D:I.83, D:Q.86, D:T.87, D:T.87, E:N.114, E:R.128, E:R.128, E:K.138, E:K.138 Water bridges: D:W.27, D:E.61, D:V.81, D:G.85, E:I.112 pi-Stacking: D:W.27, D:W.27, D:W.27 TSF.19: 19 residues within 4Å: Chain A: A.113, N.114, R.128, A.145 Chain E: S.25, W.27, H.28, G.58, A.59, I.60, E.61, V.81, V.82, I.83, R.84, G.85, Q.86, T.87, H.89 21 PLIP interactions: 17 interactions with chain E, 4 interactions with chain A Hydrophobic interactions: E:H.89 Hydrogen bonds: E:S.25, E:A.59, E:I.60, E:E.61, E:V.81, E:I.83, E:G.85, E:Q.86, E:T.87, E:T.87, A:N.114, A:R.128, A:R.128 Water bridges: E:W.27, E:I.60, E:V.81, A:I.112 pi-Stacking: E:W.27, E:W.27, E:W.27

17 x K: POTASSIUM ION(Non-covalent)

K.2: 3 residues within 4Å: Chain A: A.70, H.73, T.110 Ligand excluded by PLIP K.3: 5 residues within 4Å: Chain A: A.34, G.38, A.129, G.130, D.137 Ligand excluded by PLIP K.4: 3 residues within 4Å: Chain A: E.155, L.156, R.157 Ligand excluded by PLIP K.5: 2 residues within 4Å: Chain A: R.84, N.120 Ligand excluded by PLIP K.7: 3 residues within 4Å: Chain B: A.70, H.73, T.110 Ligand excluded by PLIP K.8: 5 residues within 4Å: Chain B: A.34, G.38, A.129, G.130, D.137 Ligand excluded by PLIP K.9: 4 residues within 4Å: Chain B: E.155, L.156, R.157, H.159 Ligand excluded by PLIP K.10: 2 residues within 4Å: Chain B: R.84, N.120 Ligand excluded by PLIP K.12: 3 residues within 4Å: Chain C: A.70, H.73, T.110 Ligand excluded by PLIP K.13: 2 residues within 4Å: Chain C: R.84, N.120 Ligand excluded by PLIP K.15: 3 residues within 4Å: Chain D: A.70, H.73, T.110 Ligand excluded by PLIP K.16: 5 residues within 4Å: Chain D: A.34, G.38, A.129, G.130, D.137 Ligand excluded by PLIP K.17: 4 residues within 4Å: Chain D: E.155, L.156, R.157, H.159 Ligand excluded by PLIP K.18: 2 residues within 4Å: Chain D: R.84, N.120 Ligand excluded by PLIP K.20: 3 residues within 4Å: Chain E: A.70, H.73, T.110 Ligand excluded by PLIP K.21: 5 residues within 4Å: Chain E: A.34, G.38, A.129, G.130, D.137 Ligand excluded by PLIP K.22: 2 residues within 4Å: Chain E: R.84, N.120 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morgunova, E. et al., Structural and Thermodynamic Insights Into the Binding Mode of Five Novel Inhibitors of Lumazine Synthase from Mycobacterium Tuberculosis. FEBS J. (2006)

Release Date

2006-12-13

Peptides

6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

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