SMTL ID : 2c97.1

LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 4-(6- chloro-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)butyl phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-pentamer

Ligands

5 x JCL: 4-(6-CHLORO-2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDIN-5-YL) BUTYL PHOSPHATE(Non-covalent)

JCL.1: 13 residues within 4Å: Chain A: W.27, H.28, G.58, A.59, V.81, V.82, I.83, G.85, Q.86, T.87, H.89, V.93 Chain B: R.128 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.59, A:V.81, A:G.85, A:Q.86, A:T.87 Water bridges: A:W.27, A:W.27, A:I.60, A:T.87, A:T.87, B:K.138, B:K.138 pi-Stacking: A:W.27, A:W.27 Salt bridges: B:R.128 JCL.10: 13 residues within 4Å: Chain B: W.27, H.28, G.58, A.59, V.81, V.82, I.83, G.85, Q.86, T.87, H.89, V.93 Chain C: R.128 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:A.59, B:V.81, B:Q.86, B:T.87 Water bridges: B:W.27, B:W.27, B:I.60, B:G.85, B:T.87, B:H.89, C:R.128 pi-Stacking: B:W.27, B:W.27 Salt bridges: C:R.128 JCL.16: 13 residues within 4Å: Chain C: W.27, H.28, G.58, A.59, V.81, V.82, I.83, G.85, Q.86, T.87, H.89, V.93 Chain D: R.128 11 PLIP interactions: 1 interactions with chain D, 10 interactions with chain C Salt bridges: D:R.128 Hydrogen bonds: C:A.59, C:V.81, C:Q.86, C:T.87 Water bridges: C:W.27, C:I.60, C:V.81, C:T.87 pi-Stacking: C:W.27, C:W.27 JCL.22: 13 residues within 4Å: Chain D: W.27, H.28, G.58, A.59, V.81, V.82, I.83, G.85, Q.86, T.87, H.89, V.93 Chain E: R.128 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:A.59, D:V.81, D:Q.86, D:T.87 Water bridges: D:S.25, D:I.60, D:V.81, D:G.85 pi-Stacking: D:W.27, D:W.27 Salt bridges: E:R.128 JCL.27: 13 residues within 4Å: Chain A: R.128 Chain E: W.27, H.28, G.58, A.59, V.81, V.82, I.83, G.85, Q.86, T.87, H.89, V.93 16 PLIP interactions: 11 interactions with chain E, 5 interactions with chain A Hydrogen bonds: E:A.59, E:V.81, E:G.85, E:Q.86, E:T.87 Water bridges: E:W.27, E:W.27, E:I.60, E:T.87, A:R.128, A:R.128, A:K.138, A:K.138 pi-Stacking: E:W.27, E:W.27 Salt bridges: A:R.128

16 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.11: 3 residues within 4Å: Chain B: A.70, H.73, T.110 Ligand excluded by PLIP K.12: 5 residues within 4Å: Chain B: A.34, G.38, A.129, G.130, D.137 Ligand excluded by PLIP K.13: 4 residues within 4Å: Chain B: E.155, L.156, R.157, H.159 Ligand excluded by PLIP K.14: 2 residues within 4Å: Chain B: R.84, N.120 Ligand excluded by PLIP K.17: 3 residues within 4Å: Chain C: A.70, H.73, T.110 Ligand excluded by PLIP K.18: 3 residues within 4Å: Chain C: E.155, L.156, R.157 Ligand excluded by PLIP K.19: 2 residues within 4Å: Chain C: R.84, N.120 Ligand excluded by PLIP K.23: 3 residues within 4Å: Chain D: A.70, H.73, T.110 Ligand excluded by PLIP K.24: 2 residues within 4Å: Chain D: R.84, N.120 Ligand excluded by PLIP K.28: 3 residues within 4Å: Chain E: A.70, H.73, T.110 Ligand excluded by PLIP K.29: 5 residues within 4Å: Chain E: A.34, G.38, A.129, G.130, D.137 Ligand excluded by PLIP K.30: 2 residues within 4Å: Chain E: R.84, N.120 Ligand excluded by PLIP

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 3 residues within 4Å: Chain A: S.26, L.57 Chain B: A.148 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.148 Hydrogen bonds: A:S.26 ACT.9: 1 residues within 4Å: Chain B: L.57 No protein-ligand interaction detected (PLIP) ACT.20: 3 residues within 4Å: Chain C: S.26, R.55, L.57 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.57 Hydrogen bonds: C:S.26, C:S.26 ACT.25: 2 residues within 4Å: Chain D: S.26, R.55 1 PLIP interactions: 1 interactions with chain D Water bridges: D:L.57 ACT.31: 2 residues within 4Å: Chain E: S.26, R.55 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.26

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

MPD.7: 7 residues within 4Å: Chain A: T.98, L.101, I.112, N.114, V.116 Chain E: Y.92, A.96 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:V.116, E:Y.92 Hydrogen bonds: A:T.98, A:T.102 MPD.8: 5 residues within 4Å: Chain A: Q.99 Chain B: Q.99 Chain C: Q.99 Chain D: Q.99 Chain E: Q.99 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: A:Q.99, D:Q.99 Hydrogen bonds: C:Q.99 Water bridges: C:Q.99, C:Q.99 MPD.15: 8 residues within 4Å: Chain A: H.89, Y.92, A.96 Chain B: V.97, T.98, L.101, I.112, N.114 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.97, B:N.114 Hydrogen bonds: A:Y.92 MPD.21: 9 residues within 4Å: Chain B: H.89, Y.92, A.96 Chain C: V.97, T.98, L.101, I.112, N.114, V.116 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.101, C:N.114, B:Y.92 Hydrogen bonds: C:T.98 MPD.26: 6 residues within 4Å: Chain C: I.60, Y.92 Chain D: V.97, T.98, L.101, N.114 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:Y.92, D:V.97, D:T.98 Hydrogen bonds: D:N.114 MPD.32: 7 residues within 4Å: Chain D: Y.92, A.96 Chain E: T.98, L.101, N.114, V.116, T.118 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: D:Y.92, E:L.101, E:V.116, E:T.118 Hydrogen bonds: E:T.98

1 x DTD: DITHIANE DIOL(Covalent)

DTD.33: 4 residues within 4Å: Chain E: K.41, V.42, G.45, C.46 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.41

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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