SMTL ID : 2c9b.2 (1 other biounit)

Lumazine Synthase from Mycobacterium tuberculosus Bound to 3-(1,3,7- TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-pentamer

Ligands

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

PUG.1: 16 residues within 4Å: Chain A: W.27, H.28, G.58, A.59, I.60, E.61, V.81, V.82, I.83, H.89, V.93 Chain B: A.113, N.114, K.138, A.142, A.145 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:N.114, B:K.138, A:A.59, A:E.61, A:V.81, A:I.83 pi-Stacking: A:W.27, A:W.27, A:W.27 PUG.4: 16 residues within 4Å: Chain B: W.27, H.28, L.57, G.58, A.59, I.60, E.61, V.81, V.82, I.83, H.89, V.93 Chain C: A.113, N.114, K.138, A.142 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:A.59, B:I.60, B:V.81, B:I.83, C:N.114, C:K.138 Water bridges: B:V.81 pi-Stacking: B:W.27, B:W.27, B:W.27 PUG.8: 13 residues within 4Å: Chain C: W.27, H.28, G.58, A.59, I.60, E.61, V.81, V.82, I.83, H.89, V.93 Chain D: A.113, N.114 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:A.59, C:I.60, C:V.81, C:I.83, D:N.114 pi-Stacking: C:W.27, C:W.27, C:W.27 PUG.11: 13 residues within 4Å: Chain D: W.27, G.58, A.59, I.60, E.61, V.81, V.82, I.83, H.89, V.93 Chain E: A.113, N.114, A.145 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:A.59, D:E.61, D:V.81, D:I.83, E:N.114 Water bridges: D:V.81, D:V.81 pi-Stacking: D:W.27, D:W.27, D:W.27 PUG.14: 17 residues within 4Å: Chain A: A.113, N.114, 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, H.89, V.93 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:S.25, E:A.59, E:I.60, E:E.61, E:V.81, E:I.83, A:N.114, A:K.138 pi-Stacking: E:W.27, E:W.27, E:W.27

6 x K: POTASSIUM ION(Non-covalent)

K.2: 3 residues within 4Å: Chain A: A.70, H.73, T.110 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.70, A:H.73, H2O.1, H2O.2 K.5: 3 residues within 4Å: Chain B: E.155, L.156, R.157 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:L.156, B:R.157 K.6: 3 residues within 4Å: Chain B: A.70, H.73, T.110 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:A.70, B:H.73 K.9: 3 residues within 4Å: Chain C: A.70, H.73, T.110 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:A.70, C:H.73 K.12: 3 residues within 4Å: Chain D: A.70, H.73, T.110 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:A.70, D:H.73, H2O.10, H2O.10 K.15: 3 residues within 4Å: Chain E: A.70, H.73, T.110 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.73, H2O.12

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 4 residues within 4Å: Chain A: G.85, Q.86, T.87 Chain B: R.128 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.85, A:Q.86, A:T.87, A:T.87 Salt bridges: B:R.128 PO4.7: 5 residues within 4Å: Chain B: G.85, Q.86, T.87, H.89 Chain C: R.128 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:G.85, B:Q.86, B:T.87 Salt bridges: C:R.128 PO4.10: 6 residues within 4Å: Chain C: G.85, Q.86, T.87, H.89 Chain D: R.128, K.138 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Q.86, C:T.87, C:T.87, C:H.89 Water bridges: D:R.128 Salt bridges: D:R.128, D:K.138 PO4.13: 5 residues within 4Å: Chain D: G.85, Q.86, T.87, H.89 Chain E: R.128 6 PLIP interactions: 1 interactions with chain E, 5 interactions with chain D Salt bridges: E:R.128 Hydrogen bonds: D:G.85, D:Q.86, D:T.87, D:H.89, D:F.90 PO4.16: 5 residues within 4Å: Chain A: R.128 Chain E: G.85, Q.86, T.87, H.89 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain E Water bridges: A:K.138 Salt bridges: A:R.128 Hydrogen bonds: E:Q.86, E:T.87, E:T.87, E:T.87

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

MPD.17: 4 residues within 4Å: Chain A: Q.99 Chain B: Q.99 Chain C: Q.99 Chain E: Q.99 1 PLIP interactions: 1 interactions with chain A Water bridges: 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
F

B
G

C
H

D
I

E
J

6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE

Related Entries With Identical Sequence