SMTL ID : 1c41.2 (2 other biounits)

CRYSTAL STRUCTURES OF A PENTAMERIC FUNGAL AND AN ICOSAHEDRAL PLANT LUMAZINE SYNTHASE REVEALS THE STRUCTURAL BASIS FOR DIFFERENCES IN ASSEMBLY

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-pentamer

Ligands

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: G.123, E.124, T.125, H.127 Chain E: R.166 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:G.123, A:E.124, A:T.125 Salt bridges: E:R.166 SO4.2: 3 residues within 4Å: Chain A: R.190 Chain B: Q.54, S.55 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.190 Hydrogen bonds: B:S.55, B:S.55 SO4.4: 5 residues within 4Å: Chain A: R.166 Chain B: G.123, E.124, T.125, H.127 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.166 Hydrogen bonds: B:E.124, B:T.125 SO4.6: 5 residues within 4Å: Chain B: R.166 Chain C: G.123, E.124, T.125, H.127 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:E.124, C:T.125 Salt bridges: B:R.166 SO4.7: 3 residues within 4Å: Chain B: R.190 Chain C: Q.54, S.55 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:V.53, C:S.55 Salt bridges: B:R.190 SO4.9: 5 residues within 4Å: Chain C: R.166 Chain D: G.123, E.124, T.125, H.127 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Salt bridges: C:R.166 Hydrogen bonds: D:E.124, D:T.125 SO4.10: 4 residues within 4Å: Chain D: R.190 Chain E: V.53, Q.54, S.55 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:S.55 Salt bridges: D:R.190 SO4.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.13: 5 residues within 4Å: Chain D: R.166 Chain E: G.123, E.124, T.125, H.127 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:E.124, E:T.125 Salt bridges: D:R.166 SO4.14: 3 residues within 4Å: Chain A: S.55 Chain E: Q.9, R.190 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:V.53, A:S.55, E:Q.9 Salt bridges: E:R.190

5 x LMZ: 5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE(Non-covalent)

LMZ.3: 14 residues within 4Å: Chain A: A.23, W.25, N.26, G.58, S.59, W.60, E.61, V.119, L.120, I.121, H.127, I.131 Chain E: I.151, F.152 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:W.25, A:W.25, A:N.26, A:S.59, A:W.60, A:V.119, A:V.119, A:I.121, E:F.152 pi-Stacking: A:W.25 LMZ.5: 14 residues within 4Å: Chain A: I.151, F.152 Chain B: A.23, W.25, N.26, G.58, S.59, W.60, E.61, V.119, L.120, I.121, H.127, I.131 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:W.25, B:W.25, B:N.26, B:S.59, B:W.60, B:V.119, B:I.121, A:F.152 pi-Stacking: B:W.25 LMZ.8: 14 residues within 4Å: Chain B: I.151, F.152 Chain C: A.23, W.25, N.26, G.58, S.59, W.60, E.61, V.119, L.120, I.121, H.127, I.131 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:W.25, C:W.25, C:N.26, C:S.59, C:W.60, C:V.119, C:I.121, B:F.152 pi-Stacking: C:W.25 LMZ.12: 12 residues within 4Å: Chain C: I.151, F.152 Chain D: W.25, G.58, S.59, W.60, E.61, V.119, L.120, I.121, H.127, I.131 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:W.25, D:W.25, D:S.59, D:W.60, D:V.119, D:I.121, C:F.152 pi-Stacking: D:W.25 LMZ.15: 13 residues within 4Å: Chain D: I.151, F.152 Chain E: W.25, N.26, G.58, S.59, W.60, E.61, V.119, L.120, I.121, H.127, I.131 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:W.25, E:W.25, E:N.26, E:S.59, E:W.60, E:V.119, E:I.121, D:F.152 pi-Stacking: E:W.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Persson, K. et al., Crystal structure analysis of a pentameric fungal and an icosahedral plant lumazine synthase reveals the structural basis for differences in assembly. Protein Sci. (1999)

Release Date

2000-08-06

Peptides

LUMAZINE SYNTHASE: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

C
H

D
I

E
J

LUMAZINE SYNTHASE

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