SMTL ID : 2vi5.1 (1 other biounit)

LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO N-6-(ribitylamino)pyrimidine-2,4(1H,3H)-dione-5-yl-propionamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-pentamer

Ligands

5 x Y19: 1-deoxy-1-{[(5S)-2,6-dioxo-5-(propanoylamino)-1,2,5,6-tetrahydropyrimidin-4-yl]amino}-D-ribitol

Y19.1: 17 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, H.89 Chain B: A.113, N.114, K.138, A.142, A.145 Ligands: PO4.4 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:N.114, B:K.138, A:S.25, A:H.28, A:A.59, A:I.60, A:E.61, A:V.81, A:I.83 Water bridges: A:V.81 Y19.5: 17 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, H.89, F.90 Chain C: A.113, N.114, A.142, A.145 Ligands: PO4.8 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.25, B:A.59, B:I.60, B:E.61, B:V.81, B:I.83, C:N.114, C:K.138 Water bridges: B:W.27, B:H.89 pi-Stacking: B:W.27 Y19.9: 16 residues within 4Å: Chain C: S.25, W.27, G.58, A.59, I.60, E.61, V.81, V.82, I.83, H.89 Chain D: A.113, N.114, K.138, A.142, A.145 Ligands: PO4.12 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:S.25, C:A.59, C:I.60, C:E.61, C:V.81, C:I.83, D:N.114, D:K.138 pi-Stacking: C:W.27 Y19.13: 17 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, H.89, F.90, V.93 Chain E: A.113, N.114, A.145 Ligands: PO4.16 12 PLIP interactions: 9 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:V.93 Hydrogen bonds: D:S.25, D:A.59, D:I.60, D:V.81, D:I.83, E:N.114, E:N.114, E:K.138 Water bridges: D:W.27, D:V.81 pi-Stacking: D:W.27 Y19.17: 17 residues within 4Å: Chain A: A.113, N.114, K.138 Chain E: S.25, W.27, H.28, G.58, A.59, I.60, E.61, V.81, V.82, I.83, H.89, F.90, V.93 Ligands: PO4.20 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain E Hydrogen bonds: A:N.114, A:K.138, E:S.25, E:A.59, E:I.60, E:V.81, E:I.83 Water bridges: A:I.112, E:E.61, E:V.81, E:H.89 Hydrophobic interactions: E:V.93 pi-Stacking: E:W.27

10 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: 3 residues within 4Å: Chain A: E.155, L.156, R.157 No protein-ligand interaction detected (PLIP) K.6: 3 residues within 4Å: Chain B: A.70, H.73, T.110 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.70, B:H.73, B:T.110, H2O.6 K.7: 3 residues within 4Å: Chain B: E.155, L.156, R.157 No protein-ligand interaction detected (PLIP) K.10: 3 residues within 4Å: Chain C: A.70, H.73, T.110 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:A.70, C:H.73, C:T.110, H2O.8 K.11: 4 residues within 4Å: Chain C: E.155, L.156, R.157, H.159 No protein-ligand interaction detected (PLIP) K.14: 3 residues within 4Å: Chain D: A.70, H.73, T.110 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:A.70, D:H.73, D:T.110, H2O.11 K.15: 3 residues within 4Å: Chain D: E.155, L.156, R.157 No protein-ligand interaction detected (PLIP) K.18: 3 residues within 4Å: Chain E: A.70, H.73, T.110 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:A.70, E:H.73, E:T.110, H2O.15 K.19: 3 residues within 4Å: Chain E: E.155, L.156, R.157 No protein-ligand interaction detected (PLIP)

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

PO4.4: 5 residues within 4Å: Chain A: G.85, Q.86, T.87 Chain B: R.128 Ligands: Y19.1 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.85, A:Q.86, A:T.87 Water bridges: A:F.90 Salt bridges: B:R.128 PO4.8: 7 residues within 4Å: Chain B: G.85, Q.86, T.87, H.89 Chain C: R.128, K.138 Ligands: Y19.5 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:G.85, B:Q.86, B:T.87, B:T.87, B:H.89 Water bridges: B:T.87, B:F.90, C:R.128, C:R.128 Salt bridges: C:R.128, C:K.138 PO4.12: 5 residues within 4Å: Chain C: G.85, Q.86, T.87 Chain D: R.128 Ligands: Y19.9 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.85, C:Q.86, C:T.87 Water bridges: C:T.87, C:T.87, C:T.87 Salt bridges: D:R.128 PO4.16: 6 residues within 4Å: Chain D: G.85, Q.86, T.87, H.89 Chain E: R.128 Ligands: Y19.13 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:G.85, D:Q.86, D:T.87 Water bridges: E:R.128, E:R.128 Salt bridges: E:R.128 PO4.20: 5 residues within 4Å: Chain A: R.128 Chain E: G.85, Q.86, T.87 Ligands: Y19.17 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:Q.86, E:T.87 Water bridges: E:G.85, E:G.85, E:H.89 Salt bridges: A:R.128, A:K.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., A New Series of N-[2,4-Dioxo-6-D-Ribitylamino-1,2, 3,4-Tetrahydropyrimidin-5-Yl]Oxalamic Acid Derivatives as Inhibitors of Lumazine Syntase and Riboflavin Synthase: Design, Synthesis, Biochemical Evaluation, Crystallography and Mechanistic Implications. J.Org.Chem. (2008)

Release Date

2008-04-08

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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