SMTL ID : 1zis.1 (3 other biounits)

Recombinant Lumazine synthase (hexagonal form)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-pentamer

Ligands

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

PO4.1: 5 residues within 4Å: Chain A: G.84, A.85, T.86, H.88 Chain E: R.127 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:G.84, A:A.85, A:T.86, A:T.86 Salt bridges: E:R.127 PO4.3: 5 residues within 4Å: Chain A: R.127 Chain B: G.84, A.85, T.86, H.88 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:R.127 Hydrogen bonds: B:G.84, B:A.85, B:T.86 PO4.5: 5 residues within 4Å: Chain B: R.127 Chain C: G.84, A.85, T.86, H.88 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.84, C:A.85, C:T.86 Salt bridges: B:R.127 PO4.7: 4 residues within 4Å: Chain C: R.127 Chain D: G.84, A.85, T.86 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:A.85, D:T.86 Salt bridges: C:R.127 PO4.8: 5 residues within 4Å: Chain D: R.127 Chain E: G.84, A.85, T.86, H.88 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain E Salt bridges: D:R.127 Hydrogen bonds: E:A.85, E:T.86, E:T.86

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

INI.2: 14 residues within 4Å: Chain A: F.22, N.23, G.55, A.56, F.57, E.58, T.80, V.81, I.82, H.88, V.92 Chain E: I.112, F.113, K.135 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:N.23, A:A.56, A:F.57, A:T.80, A:I.82, E:F.113, E:K.135 pi-Stacking: A:F.22 INI.4: 14 residues within 4Å: Chain A: I.112, F.113, K.135 Chain B: F.22, N.23, G.55, A.56, F.57, E.58, T.80, V.81, I.82, H.88, V.92 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:F.113, A:K.135, B:N.23, B:A.56, B:F.57, B:T.80, B:I.82 pi-Stacking: B:F.22 INI.6: 14 residues within 4Å: Chain B: I.112, F.113, K.135 Chain C: F.22, N.23, G.55, A.56, F.57, E.58, T.80, V.81, I.82, H.88, V.92 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:N.23, C:A.56, C:F.57, C:T.80, C:I.82, C:I.82, B:F.113, B:K.135 pi-Stacking: C:F.22 INI.9: 14 residues within 4Å: Chain C: I.112, F.113, K.135 Chain D: F.22, N.23, G.55, A.56, F.57, E.58, T.80, V.81, I.82, H.88, V.92 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:N.23, D:A.56, D:F.57, D:T.80, D:I.82, C:F.113, C:K.135 pi-Stacking: D:F.22 INI.10: 14 residues within 4Å: Chain D: I.112, F.113, K.135 Chain E: F.22, N.23, G.55, A.56, F.57, E.58, T.80, V.81, I.82, H.88, V.92 8 PLIP interactions: 6 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:N.23, E:A.56, E:F.57, E:T.80, E:I.82, D:F.113, D:K.135 pi-Stacking: E:F.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lopez-Jaramillo, F.J., Crystal structure of recombinant Lumazine synthase (hexagonal form). To be Published

Release Date

2006-10-03

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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