SMTL ID : 1w19.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-10-mer

Ligands

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

ACY.1: 3 residues within 4Å: Chain A: S.26, V.56, L.57 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.26 ACY.7: 3 residues within 4Å: Chain B: S.26, V.56 Chain C: A.148 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.26 Hydrophobic interactions: C:A.148 ACY.13: 0 residues within 4Å: (No contacts) 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Water bridges: D:T.152, C:S.26, C:S.26 ACY.19: 2 residues within 4Å: Chain D: S.26, R.55 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.26 ACY.24: 2 residues within 4Å: Chain E: V.56, L.57 No protein-ligand interaction detected (PLIP) ACY.30: 3 residues within 4Å: Chain F: S.26, V.56, L.57 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.26 ACY.36: 3 residues within 4Å: Chain G: S.26, V.56 Chain H: A.148 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:A.148 Hydrogen bonds: G:S.26 ACY.42: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain H Water bridges: H:S.26, H:S.26 ACY.48: 2 residues within 4Å: Chain I: S.26, R.55 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:S.26 ACY.53: 2 residues within 4Å: Chain J: V.56, L.57 1 PLIP interactions: 1 interactions with chain F Water bridges: F:T.152

4 x DTU: (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL(Non-covalent)

DTU.2: 6 residues within 4Å: Chain A: D.14, A.15, C.46, V.144, L.147, A.148 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.14, A:D.14 DTU.8: 5 residues within 4Å: Chain B: C.46, V.144, L.147, A.148, L.151 No protein-ligand interaction detected (PLIP) DTU.31: 6 residues within 4Å: Chain F: D.14, A.15, C.46, V.144, L.147, A.148 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.14 DTU.37: 5 residues within 4Å: Chain G: C.46, V.144, L.147, A.148, L.151 No protein-ligand interaction detected (PLIP)

2 x T1P: 3-{2,6,8-TRIOXO-9-[(2R,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}PROPYL DIHYDROGEN PHOSPHATE(Non-covalent)

T1P.3: 18 residues within 4Å: Chain A: 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, K.138, A.142 21 PLIP interactions: 4 interactions with chain B, 17 interactions with chain A Hydrogen bonds: B:N.114, B:K.138, A:A.59, A:I.60, A:E.61, A:V.81, A:I.83, A:G.85, A:Q.86, A:T.87, A:T.87 Water bridges: B:R.128, A:W.27, A:V.81, A:Q.86, A:F.90 Salt bridges: B:R.128 pi-Stacking: A:W.27, A:W.27, A:W.27, A:W.27 T1P.32: 18 residues within 4Å: Chain F: 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, K.138, A.142 21 PLIP interactions: 17 interactions with chain F, 4 interactions with chain G Hydrogen bonds: F:A.59, F:I.60, F:E.61, F:V.81, F:I.83, F:G.85, F:Q.86, F:T.87, G:N.114, G:K.138 Water bridges: F:W.27, F:V.81, F:Q.86, F:T.87, F:F.90, G:R.128 pi-Stacking: F:W.27, F:W.27, F:W.27, F:W.27 Salt bridges: G:R.128

26 x K: POTASSIUM ION(Non-covalent)

K.4: 3 residues within 4Å: Chain A: A.70, H.73, T.110 Ligand excluded by PLIP K.5: 5 residues within 4Å: Chain A: A.34, G.38, A.129, G.130, D.137 Ligand excluded by PLIP K.6: 7 residues within 4Å: Chain A: L.156, R.157 Chain F: E.155, L.156, R.157, H.159 Ligands: K.35 Ligand excluded by PLIP K.10: 3 residues within 4Å: Chain B: A.70, H.73, T.110 Ligand excluded by PLIP K.11: 5 residues within 4Å: Chain B: A.34, G.38, A.129, G.130, D.137 Ligand excluded by PLIP K.12: 7 residues within 4Å: Chain B: E.155, L.156, R.157, H.159 Chain J: L.156, R.157, H.159 Ligand excluded by PLIP K.16: 3 residues within 4Å: Chain C: A.70, H.73, T.110 Ligand excluded by PLIP K.17: 5 residues within 4Å: Chain C: A.34, G.38, A.129, G.130, D.137 Ligand excluded by PLIP K.18: 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.22: 3 residues within 4Å: Chain D: A.70, H.73, T.110 Ligand excluded by PLIP K.23: 5 residues within 4Å: Chain D: A.34, G.38, A.129, G.130, D.137 Ligand excluded by PLIP K.27: 3 residues within 4Å: Chain E: A.70, H.73, T.110 Ligand excluded by PLIP K.28: 5 residues within 4Å: Chain E: A.34, G.38, A.129, G.130, D.137 Ligand excluded by PLIP K.33: 3 residues within 4Å: Chain F: A.70, H.73, T.110 Ligand excluded by PLIP K.34: 5 residues within 4Å: Chain F: A.34, G.38, A.129, G.130, D.137 Ligand excluded by PLIP K.35: 7 residues within 4Å: Chain A: E.155, L.156, R.157, H.159 Chain F: L.156, R.157 Ligands: K.6 Ligand excluded by PLIP K.39: 3 residues within 4Å: Chain G: A.70, H.73, T.110 Ligand excluded by PLIP K.40: 5 residues within 4Å: Chain G: A.34, G.38, A.129, G.130, D.137 Ligand excluded by PLIP K.41: 7 residues within 4Å: Chain E: L.156, R.157, H.159 Chain G: E.155, L.156, R.157, H.159 Ligand excluded by PLIP K.45: 3 residues within 4Å: Chain H: A.70, H.73, T.110 Ligand excluded by PLIP K.46: 5 residues within 4Å: Chain H: A.34, G.38, A.129, G.130, D.137 Ligand excluded by PLIP K.47: 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.51: 3 residues within 4Å: Chain I: A.70, H.73, T.110 Ligand excluded by PLIP K.52: 5 residues within 4Å: Chain I: A.34, G.38, A.129, G.130, D.137 Ligand excluded by PLIP K.56: 3 residues within 4Å: Chain J: A.70, H.73, T.110 Ligand excluded by PLIP K.57: 5 residues within 4Å: Chain J: A.34, G.38, A.129, G.130, D.137 Ligand excluded by PLIP

2 x T2P: 3-{2,6,8-TRIOXO-9-[(2S,3R,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}PROPYL DIHYDROGEN PHOSPHATE(Non-covalent)

T2P.9: 18 residues within 4Å: Chain B: 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 19 PLIP interactions: 14 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, C:N.114, C:K.138 Water bridges: B:V.81, B:G.85, B:F.90, C:N.114, C:K.138 pi-Stacking: B:W.27, B:W.27, B:W.27 Salt bridges: C:R.128 T2P.38: 18 residues within 4Å: Chain G: 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: 15 interactions with chain G, 5 interactions with chain H Hydrogen bonds: 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, H:N.114, H:K.138 Water bridges: G:V.81, G:G.85, G:F.90, H:N.114, H:K.138 pi-Stacking: G:W.27, G:W.27, G:W.27 Salt bridges: H:R.128

6 x DTV: (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL(Non-covalent)

DTV.14: 4 residues within 4Å: Chain C: A.15, C.46, A.148, L.151 No protein-ligand interaction detected (PLIP) DTV.20: 7 residues within 4Å: Chain D: D.14, A.15, C.46, V.144, L.147, A.148, L.151 No protein-ligand interaction detected (PLIP) DTV.25: 5 residues within 4Å: Chain E: A.15, C.46, V.144, L.151 Ligands: D1D.29 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:V.144 DTV.43: 4 residues within 4Å: Chain H: A.15, C.46, A.148, L.151 No protein-ligand interaction detected (PLIP) DTV.49: 7 residues within 4Å: Chain I: D.14, A.15, C.46, V.144, L.147, A.148, L.151 No protein-ligand interaction detected (PLIP) DTV.54: 5 residues within 4Å: Chain J: A.15, C.46, V.144, L.151 Ligands: D1D.58 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:V.144

2 x T5P: 3-{2,6,8-TRIOXO-9-[(2S,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}PROPYL DIHYDROGEN PHOSPHATE(Non-covalent)

T5P.15: 18 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 21 PLIP interactions: 5 interactions with chain D, 16 interactions with chain C Hydrogen bonds: D:N.114, D:K.138, C:S.25, C:A.59, C:I.60, C:E.61, C:V.81, C:I.83, C:Q.86, C:T.87 Water bridges: D:I.112, D:R.128, C:W.27, C:W.27, C:E.61, C:G.85, C:Q.86 Salt bridges: D:R.128 pi-Stacking: C:W.27, C:W.27, C:W.27 T5P.44: 18 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 21 PLIP interactions: 16 interactions with chain H, 5 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, I:K.138 Water bridges: H:W.27, H:W.27, H:E.61, H:G.85, H:Q.86, I:I.112, I:R.128 pi-Stacking: H:W.27, H:W.27, H:W.27 Salt bridges: I:R.128

4 x T4P: 3-{2,6,8-TRIOXO-9-[(2R,3R,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}PROPYL DIHYDROGEN PHOSPHATE(Non-covalent)

T4P.21: 18 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 18 PLIP interactions: 3 interactions with chain E, 15 interactions with chain D Hydrogen bonds: E:N.114, E:K.138, D:S.25, D:G.58, D:A.59, D:I.60, D:V.81, D:I.83, D:Q.86, D:T.87 Salt bridges: E:R.128 Water bridges: D:W.27, D:V.81, D:G.85, D:G.85 pi-Stacking: D:W.27, D:W.27, D:W.27 T4P.26: 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 22 PLIP interactions: 17 interactions with chain E, 5 interactions with chain A Hydrogen bonds: E:S.25, E:G.58, E:A.59, E:I.60, E:V.81, E:I.83, E:Q.86, E:T.87, E:H.89, A:N.114, A:K.138 Water bridges: E:V.81, E:G.85, E:T.87, E:T.87, E:F.90, A:R.128, A:R.128 pi-Stacking: E:W.27, E:W.27, E:W.27 Salt bridges: A:R.128 T4P.50: 18 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 18 PLIP interactions: 15 interactions with chain I, 3 interactions with chain J Hydrogen bonds: I:S.25, I:G.58, 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:V.81, I:G.85, I:G.85 pi-Stacking: I:W.27, I:W.27, I:W.27 Salt bridges: J:R.128 T4P.55: 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 20 PLIP interactions: 15 interactions with chain J, 5 interactions with chain F Hydrogen bonds: J:S.25, J:G.58, J:A.59, J:I.60, J:V.81, J:I.83, J:Q.86, J:T.87, J:H.89, F:N.114, F:K.138 Water bridges: J:V.81, J:G.85, J:F.90, F:R.128, F:R.128 pi-Stacking: J:W.27, J:W.27, J:W.27 Salt bridges: F:R.128

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

D1D.29: 4 residues within 4Å: Chain E: V.42, G.45, C.46 Ligands: DTV.25 No protein-ligand interaction detected (PLIP) D1D.58: 4 residues within 4Å: Chain J: V.42, G.45, C.46 Ligands: DTV.54 No protein-ligand interaction detected (PLIP)

Links

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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

2005-03-02

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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