SMTL ID : 1ejb.1

LUMAZINE SYNTHASE FROM SACCHAROMYCES CEREVISIAE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-pentamer

Ligands

5 x INJ: 5-(6-D-RIBITYLAMINO-2,4-DIHYDROXYPYRIMIDIN-5-YL)-1-PENTYL-PHOSPHONIC ACID(Non-covalent)

INJ.1: 18 residues within 4Å: Chain A: W.26, N.27, G.59, S.60, Y.61, E.62, V.89, L.90, I.91, G.93, S.94, T.95, H.97, I.101 Chain B: I.121, F.122, R.136, W.152 19 PLIP interactions: 4 interactions with chain B, 15 interactions with chain A Hydrogen bonds: B:F.122, B:R.136, A:N.27, A:S.60, A:Y.61, A:V.89, A:I.91, A:S.94, A:T.95 Water bridges: B:V.120, B:L.124, A:W.26, A:E.62, A:V.89, A:H.97, A:F.98 Hydrophobic interactions: A:L.90 pi-Stacking: A:W.26, A:W.26 INJ.2: 17 residues within 4Å: Chain B: W.26, N.27, G.59, S.60, Y.61, E.62, V.89, L.90, I.91, G.93, S.94, T.95, I.101 Chain C: I.121, F.122, R.136, W.152 22 PLIP interactions: 17 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:W.26, B:L.90 Hydrogen bonds: B:N.27, B:S.60, B:Y.61, B:V.89, B:I.91, B:S.94, B:T.95, C:F.122, C:R.136 Water bridges: B:W.26, B:E.62, B:V.89, B:T.95, B:H.97, B:F.98, C:V.120, C:L.124, C:R.136 pi-Stacking: B:W.26, B:W.26 INJ.3: 17 residues within 4Å: Chain C: W.26, N.27, G.59, S.60, Y.61, E.62, V.89, L.90, I.91, G.93, S.94, T.95, I.101 Chain D: I.121, F.122, R.136, W.152 21 PLIP interactions: 17 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:W.26, C:L.90 Hydrogen bonds: C:N.27, C:S.60, C:Y.61, C:V.89, C:I.91, C:S.94, C:T.95, D:F.122, D:R.136 Water bridges: C:E.62, C:V.89, C:G.93, C:T.95, C:H.97, C:H.97, D:V.120, D:W.152 pi-Stacking: C:W.26, C:W.26 INJ.4: 18 residues within 4Å: Chain D: W.26, N.27, G.59, S.60, Y.61, E.62, V.89, L.90, I.91, G.93, S.94, T.95, H.97, I.101 Chain E: I.121, F.122, R.136, W.152 19 PLIP interactions: 17 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:W.26, D:L.90, D:H.97 Hydrogen bonds: D:N.27, D:S.60, D:Y.61, D:V.89, D:I.91, D:S.94, D:T.95, E:F.122, E:R.136 Water bridges: D:W.26, D:E.62, D:E.62, D:V.89, D:G.93 pi-Stacking: D:W.26, D:W.26 INJ.5: 18 residues within 4Å: Chain A: I.121, F.122, R.136, W.152 Chain E: W.26, N.27, G.59, S.60, Y.61, E.62, V.89, L.90, I.91, G.93, S.94, T.95, H.97, I.101 18 PLIP interactions: 14 interactions with chain E, 4 interactions with chain A Hydrophobic interactions: E:W.26, E:L.90 Hydrogen bonds: E:N.27, E:S.60, E:Y.61, E:V.89, E:I.91, E:S.94, E:T.95, A:F.122, A:R.136 Water bridges: E:E.62, E:V.89, E:V.89, A:V.120, A:R.136 pi-Stacking: E:W.26, E:W.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meining, W. et al., The atomic structure of pentameric lumazine synthase from Saccharomyces cerevisiae at 1.85 A resolution reveals the binding mode of a phosphonate intermediate analogue. J.Mol.Biol. (2000)

Release Date

2001-03-02

Peptides

LUMAZINE SYNTHASE: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

LUMAZINE SYNTHASE