SMTL ID : 2c92.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-pentamer

Ligands

5 x TP6: 3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL) 1-PHOSPHATE(Non-covalent)

TP6.1: 20 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, F.90 Chain B: A.113, N.114, R.128, K.138, A.142, A.145 21 PLIP interactions: 17 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:T.87, B:N.114, B:K.138 Water bridges: A:W.27, 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 TP6.5: 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, F.90 Chain C: A.113, N.114, R.128, A.142, A.145 20 PLIP interactions: 17 interactions with chain B, 3 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:K.138 Water bridges: B:W.27, B:W.27, B:H.28, B:H.89, B:H.89 pi-Stacking: B:W.27, B:W.27, B:W.27 Salt bridges: C:R.128 TP6.9: 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, F.90 Chain D: A.113, N.114, R.128, K.138, A.142, A.145 21 PLIP interactions: 16 interactions with chain C, 5 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, C:T.87, D:N.114, D:K.138, D:K.138 Water bridges: C:W.27, C:V.81, C:G.85, C:G.85, D:R.128 pi-Stacking: C:W.27, C:W.27, C:W.27 Salt bridges: D:R.128 TP6.13: 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, G.85, Q.86, T.87, F.90 Chain E: A.113, N.114, R.128, K.138, A.142, A.145 22 PLIP interactions: 17 interactions with chain D, 5 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:K.138, E:K.138 Water bridges: D:W.27, D:E.61, D:V.81, D:G.85, D:G.85, E:I.112 pi-Stacking: D:W.27, D:W.27, D:W.27 Salt bridges: E:R.128 TP6.17: 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, F.90 21 PLIP interactions: 17 interactions with chain E, 4 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, A:N.114, A:K.138 Water bridges: E:W.27, E:H.28, E:E.61, E:G.85, E:T.87, A:I.112 pi-Stacking: E:W.27, E:W.27, E:W.27 Salt bridges: A:R.128

13 x K: POTASSIUM ION(Non-covalent)

K.2: 3 residues within 4Å: Chain A: A.70, H.73, T.110 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.70, A:H.73, A:T.110, H2O.2, H2O.3 K.3: 5 residues within 4Å: Chain A: A.34, G.38, A.129, G.130, D.137 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:A.34, A:A.129, A:G.130, A:D.137 K.4: 4 residues within 4Å: Chain A: E.155, L.156, R.157, H.159 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.156, A:R.157, H2O.6 K.6: 3 residues within 4Å: Chain B: A.70, H.73, T.110 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.70, B:H.73, B:T.110, H2O.8, H2O.9 K.7: 5 residues within 4Å: Chain B: A.34, G.38, A.129, G.130, D.137 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.34, B:A.129, B:G.130, B:D.137, H2O.7 K.8: 4 residues within 4Å: Chain B: E.155, L.156, R.157, H.159 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:L.156, B:R.157, H2O.11 K.10: 3 residues within 4Å: Chain C: A.70, H.73, T.110 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:A.70, C:H.73, H2O.12, H2O.13, H2O.14 K.11: 4 residues within 4Å: Chain C: A.34, G.38, A.129, G.130 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:A.34, C:G.130 K.12: 4 residues within 4Å: Chain C: E.155, L.156, R.157, H.159 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:L.156, C:R.157, H2O.16, H2O.16 K.14: 3 residues within 4Å: Chain D: A.70, H.73, T.110 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:A.70, D:H.73, D:T.110, H2O.17, H2O.18 K.15: 5 residues within 4Å: Chain D: A.34, G.38, A.129, G.130, D.137 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:A.34, D:G.130, H2O.17 K.18: 3 residues within 4Å: Chain E: A.70, H.73, T.110 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:A.70, E:H.73, E:T.110, H2O.22, H2O.23 K.19: 5 residues within 4Å: Chain E: A.34, G.38, A.129, G.130, D.137 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:A.129, E:G.130, E:D.137, H2O.21, H2O.21

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

DTU.16: 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) DTU.20: 5 residues within 4Å: Chain E: A.15, C.46, L.147, A.148, L.151 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:A.15, E:V.144

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.21: 5 residues within 4Å: Chain A: Q.99 Chain B: Q.99 Chain C: Q.99 Chain D: Q.99 Chain E: Q.99 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain A Water bridges: E:Q.99, A:Q.99, A:Q.99 Hydrogen bonds: A:Q.99

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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