SMTL ID : 1w29.1

Lumazine Synthase from Mycobacterium tuberculosis bound to 3-(1,3,7- trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)butane 1-phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-10-mer

Ligands

8 x ACY: ACETIC ACID(Non-functional Binders)

ACY.1: 4 residues within 4Å: Chain A: S.26, R.55, V.56, L.57 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.57 Hydrogen bonds: A:R.55 ACY.6: 2 residues within 4Å: Chain B: R.55 Chain C: A.148 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.26, B:L.57 ACY.15: 2 residues within 4Å: Chain D: V.56, L.57 1 PLIP interactions: 1 interactions with chain D Water bridges: D:R.55 ACY.19: 3 residues within 4Å: Chain E: R.55, V.56, L.57 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:L.57 ACY.24: 4 residues within 4Å: Chain F: S.26, R.55, V.56, L.57 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:L.57 Hydrogen bonds: F:R.55 ACY.29: 2 residues within 4Å: Chain G: R.55 Chain H: A.148 2 PLIP interactions: 2 interactions with chain G Water bridges: G:S.26, G:L.57 ACY.38: 2 residues within 4Å: Chain I: V.56, L.57 1 PLIP interactions: 1 interactions with chain I Water bridges: I:R.55 ACY.42: 3 residues within 4Å: Chain J: R.55, V.56, L.57 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain J Water bridges: F:T.152 Hydrophobic interactions: J:L.57

8 x TS1: 4-{2,6,8-TRIOXO-9-[(2R,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL DIHYDROGEN PHOSPHATE(Non-covalent)

TS1.2: 21 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, G.85, Q.86, T.87, H.89 Chain B: A.113, N.114, R.128, E.136, K.138, A.142, A.145 20 PLIP interactions: 16 interactions with chain A, 4 interactions with chain B Hydrogen bonds: 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:H.89, B:N.114, B:K.138 Water bridges: A:V.81, A:G.85, A:G.85, A:T.87, B:R.128 pi-Stacking: A:W.27, A:W.27, A:W.27 Salt bridges: B:R.128 TS1.7: 19 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, G.85, Q.86, T.87, H.89 Chain C: A.113, N.114, R.128, K.138, A.145 18 PLIP interactions: 14 interactions with chain B, 4 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, C:N.114 Water bridges: B:V.81, B:V.81, B:T.87, B:F.90, C:K.138, C:K.138 pi-Stacking: B:W.27, B:W.27 Salt bridges: C:R.128 TS1.11: 20 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.142, A.145 18 PLIP interactions: 14 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:S.25, C:A.59, C:I.60, C:E.61, C:V.81, C:I.83, C:Q.86, C:T.87, D:N.114 Water bridges: C:W.27, C:T.87, D:K.138, D:K.138 pi-Stacking: C:W.27, C:W.27, C:W.27, C:W.27 Salt bridges: D:R.128 TS1.20: 20 residues within 4Å: Chain A: A.113, N.114, R.128, K.138, A.142, A.145 Chain E: 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 21 PLIP interactions: 18 interactions with chain E, 3 interactions with chain A Hydrogen bonds: E:S.25, E:A.59, E:I.60, E:E.61, E:V.81, E:I.83, E:Q.86, E:T.87, E:T.87, E:T.87, A:N.114, A:K.138 Water bridges: E:W.27, E:V.81, E:G.85, E:G.85 pi-Stacking: E:W.27, E:W.27, E:W.27, E:W.27 Salt bridges: A:R.128 TS1.25: 21 residues within 4Å: Chain F: 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 G: A.113, N.114, R.128, E.136, K.138, A.142, A.145 20 PLIP interactions: 17 interactions with chain F, 3 interactions with chain G Hydrogen bonds: F:S.25, F:A.59, F:I.60, F:E.61, F:V.81, F:I.83, F:Q.86, F:T.87, F:H.89, G:N.114, G:K.138 Water bridges: F:V.81, F:G.85, F:T.87, F:T.87, F:H.89 pi-Stacking: F:W.27, F:W.27, F:W.27 Salt bridges: G:R.128 TS1.30: 19 residues within 4Å: Chain G: 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 H: A.113, N.114, R.128, K.138, A.145 20 PLIP interactions: 4 interactions with chain H, 16 interactions with chain G Hydrogen bonds: H:N.114, G:S.25, G:A.59, G:I.60, G:E.61, G:V.81, G:I.83, G:Q.86, G:T.87, G:H.89 Water bridges: H:K.138, H:K.138, G:V.81, G:V.81, G:T.87, G:T.87, G:F.90 Salt bridges: H:R.128 pi-Stacking: G:W.27, G:W.27 TS1.34: 20 residues within 4Å: Chain H: 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 I: A.113, N.114, R.128, K.138, A.142, A.145 18 PLIP interactions: 14 interactions with chain H, 4 interactions with chain I Hydrogen bonds: H:S.25, H:A.59, H:I.60, H:E.61, H:V.81, H:I.83, H:Q.86, H:T.87, I:N.114 Water bridges: H:W.27, H:G.85, I:K.138, I:K.138 pi-Stacking: H:W.27, H:W.27, H:W.27, H:W.27 Salt bridges: I:R.128 TS1.43: 20 residues within 4Å: Chain F: A.113, N.114, R.128, K.138, A.142, A.145 Chain J: 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 21 PLIP interactions: 18 interactions with chain J, 3 interactions with chain F Hydrogen bonds: J:S.25, J:A.59, J:I.60, J:E.61, J:V.81, J:I.83, J:Q.86, J:T.87, J:T.87, J:T.87, F:N.114, F:K.138 Water bridges: J:W.27, J:V.81, J:G.85, J:T.87 pi-Stacking: J:W.27, J:W.27, J:W.27, J:W.27 Salt bridges: F:R.128

26 x K: POTASSIUM ION(Non-covalent)

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: A.70, H.73, T.110 Ligand excluded by PLIP K.5: 8 residues within 4Å: Chain A: E.155, L.156, R.157, H.159 Chain F: L.156, R.157, H.159 Ligands: K.28 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: 3 residues within 4Å: Chain B: A.70, H.73, T.110 Ligand excluded by PLIP K.10: 6 residues within 4Å: Chain B: E.155, L.156, R.157 Chain J: E.155, L.156, R.157 Ligand excluded by PLIP K.12: 5 residues within 4Å: Chain C: A.34, G.38, A.129, G.130, D.137 Ligand excluded by PLIP K.13: 3 residues within 4Å: Chain C: A.70, H.73, T.110 Ligand excluded by PLIP K.14: 8 residues within 4Å: Chain C: E.155, L.156, R.157, H.159 Chain I: E.155, L.156, R.157, H.159 Ligand excluded by PLIP K.17: 5 residues within 4Å: Chain D: A.34, G.38, A.129, G.130, D.137 Ligand excluded by PLIP K.18: 3 residues within 4Å: Chain D: 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: 3 residues within 4Å: Chain E: A.70, H.73, T.110 Ligand excluded by PLIP K.26: 5 residues within 4Å: Chain F: A.34, G.38, A.129, G.130, D.137 Ligand excluded by PLIP K.27: 3 residues within 4Å: Chain F: A.70, H.73, T.110 Ligand excluded by PLIP K.28: 8 residues within 4Å: Chain A: L.156, R.157, H.159 Chain F: E.155, L.156, R.157, H.159 Ligands: K.5 Ligand excluded by PLIP K.31: 5 residues within 4Å: Chain G: A.34, G.38, A.129, G.130, D.137 Ligand excluded by PLIP K.32: 3 residues within 4Å: Chain G: A.70, H.73, T.110 Ligand excluded by PLIP K.33: 6 residues within 4Å: Chain E: E.155, L.156, R.157 Chain G: E.155, L.156, R.157 Ligand excluded by PLIP K.35: 5 residues within 4Å: Chain H: A.34, G.38, A.129, G.130, D.137 Ligand excluded by PLIP K.36: 3 residues within 4Å: Chain H: A.70, H.73, T.110 Ligand excluded by PLIP K.37: 8 residues within 4Å: Chain D: E.155, L.156, R.157, H.159 Chain H: E.155, L.156, R.157, H.159 Ligand excluded by PLIP K.40: 5 residues within 4Å: Chain I: A.34, G.38, A.129, G.130, D.137 Ligand excluded by PLIP K.41: 3 residues within 4Å: Chain I: A.70, H.73, T.110 Ligand excluded by PLIP K.44: 5 residues within 4Å: Chain J: A.34, G.38, A.129, G.130, D.137 Ligand excluded by PLIP K.45: 3 residues within 4Å: Chain J: A.70, H.73, T.110 Ligand excluded by PLIP

2 x TS0: 4-{2,6,8-TRIOXO-9-[(2S,3R,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL DIHYDROGEN PHOSPHATE(Non-covalent)

TS0.16: 19 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, G.85, Q.86, T.87, H.89 Chain E: A.113, N.114, R.128, K.138, A.142 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:S.25, D:A.59, D:I.60, D:V.81, D:I.83, D:Q.86, D:T.87, E:N.114, E:K.138 Water bridges: D:W.27, D:H.89, D:H.89 pi-Stacking: D:W.27, D:W.27, D:W.27 Salt bridges: E:R.128 TS0.39: 19 residues within 4Å: Chain I: 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 J: A.113, N.114, R.128, K.138, A.142 16 PLIP interactions: 13 interactions with chain I, 3 interactions with chain J Hydrogen bonds: I:S.25, I:A.59, I:I.60, I:V.81, I:I.83, I:Q.86, I:T.87, J:N.114, J:K.138 Water bridges: I:W.27, I:H.89, I:H.89 pi-Stacking: I:W.27, I:W.27, I:W.27 Salt bridges: J:R.128

2 x D1D: (4S,5S)-1,2-DITHIANE-4,5-DIOL(Non-covalent)

D1D.23: 3 residues within 4Å: Chain E: V.42, G.45, C.46 No protein-ligand interaction detected (PLIP) D1D.46: 3 residues within 4Å: Chain J: V.42, G.45, C.46 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morgunova, E. et al., Crystal Structure of Lumazine Synthase from Mycobacterium Tuberculosis as a Target for Rational Drug Design: Binding Mode of a New Class of Purinetrione Inhibitors(,). Biochemistry (2005)

Release Date

2005-03-03

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
A

G
B

H
C

I
D

J
E

6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

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