SMTL ID : 1c2y.1 (1 other biounit)

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 3.30 Å

Oligo State

homo-20-mer

Ligands

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

LMZ.1: 13 residues within 4Å: Chain A: A.21, F.23, N.24, G.55, A.56, Y.57, E.58, A.80, V.81, V.92 Chain E: V.112, F.113, K.135 9 PLIP interactions: 3 interactions with chain E, 6 interactions with chain A Hydrogen bonds: E:F.113, E:K.135, E:K.135, A:N.24, A:A.56, A:Y.57, A:A.80, A:V.82 pi-Stacking: A:F.23 LMZ.2: 12 residues within 4Å: Chain A: V.112, F.113 Chain B: F.23, N.24, G.55, A.56, Y.57, E.58, A.80, V.81, V.82, V.92 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.24, B:A.56, B:Y.57, B:A.80, B:A.80, B:V.82, A:F.113 pi-Stacking: B:F.23 LMZ.3: 13 residues within 4Å: Chain B: V.112, F.113 Chain C: A.21, F.23, N.24, G.55, A.56, Y.57, E.58, A.80, V.81, V.82, V.92 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.24, C:A.56, C:Y.57, C:A.80, C:V.82, B:F.113 pi-Stacking: C:F.23 LMZ.4: 13 residues within 4Å: Chain C: V.112, F.113 Chain D: A.21, F.23, N.24, G.55, A.56, Y.57, E.58, A.80, V.81, H.88, V.92 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:F.113, D:N.24, D:A.56, D:Y.57, D:A.80, D:V.82 pi-Stacking: D:F.23 LMZ.5: 13 residues within 4Å: Chain D: V.112, F.113, K.135 Chain E: F.23, N.24, G.55, A.56, Y.57, E.58, A.80, V.81, H.88, V.92 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:N.24, E:A.56, E:Y.57, E:A.80, D:F.113, D:K.135 pi-Stacking: E:F.23 LMZ.6: 13 residues within 4Å: Chain F: A.21, F.23, N.24, G.55, A.56, Y.57, E.58, A.80, V.81, V.82, V.92 Chain J: V.112, F.113 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain J Hydrogen bonds: F:N.24, F:A.56, F:Y.57, F:A.80, F:V.82, J:F.113 pi-Stacking: F:F.23 LMZ.7: 13 residues within 4Å: Chain F: V.112, F.113 Chain G: A.21, F.23, N.24, G.55, A.56, Y.57, E.58, A.80, V.81, V.82, V.92 8 PLIP interactions: 7 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:N.24, G:A.56, G:Y.57, G:A.80, G:A.80, G:V.82, F:F.113 pi-Stacking: G:F.23 LMZ.8: 14 residues within 4Å: Chain G: V.112, F.113, K.135 Chain H: A.21, F.23, N.24, G.55, A.56, Y.57, E.58, A.80, V.81, V.82, V.92 8 PLIP interactions: 6 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:N.24, H:A.56, H:Y.57, H:A.80, H:V.82, G:F.113, G:K.135 pi-Stacking: H:F.23 LMZ.9: 13 residues within 4Å: Chain H: V.112, F.113 Chain I: A.21, F.23, N.24, G.55, A.56, Y.57, E.58, A.80, V.81, V.82, V.92 8 PLIP interactions: 7 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:N.24, I:A.56, I:Y.57, I:A.80, I:V.82, I:H.88, H:F.113 pi-Stacking: I:F.23 LMZ.10: 14 residues within 4Å: Chain I: V.112, F.113, K.135 Chain J: A.21, F.23, N.24, G.55, A.56, Y.57, E.58, A.80, V.81, V.82, V.92 9 PLIP interactions: 6 interactions with chain J, 3 interactions with chain I Hydrogen bonds: J:N.24, J:A.56, J:Y.57, J:A.80, J:V.82, I:F.113, I:K.135, I:K.135 pi-Stacking: J:F.23 LMZ.11: 14 residues within 4Å: Chain K: A.21, F.23, N.24, G.55, A.56, Y.57, E.58, A.80, V.81, V.82, H.88, V.92 Chain O: V.112, F.113 7 PLIP interactions: 1 interactions with chain O, 6 interactions with chain K Hydrogen bonds: O:F.113, K:N.24, K:A.56, K:Y.57, K:A.80, K:V.82 pi-Stacking: K:F.23 LMZ.12: 13 residues within 4Å: Chain K: V.112, F.113, K.135 Chain L: F.23, N.24, G.55, A.56, Y.57, E.58, A.80, V.81, V.82, V.92 9 PLIP interactions: 2 interactions with chain K, 7 interactions with chain L Hydrogen bonds: K:F.113, K:K.135, L:N.24, L:A.56, L:Y.57, L:A.80, L:A.80, L:V.82 pi-Stacking: L:F.23 LMZ.13: 12 residues within 4Å: Chain L: V.112, F.113 Chain M: F.23, N.24, G.55, A.56, Y.57, E.58, A.80, V.81, V.82, V.92 10 PLIP interactions: 3 interactions with chain L, 7 interactions with chain M Hydrogen bonds: L:F.113, L:K.135, L:K.135, M:N.24, M:A.56, M:Y.57, M:A.80, M:A.80, M:V.82 pi-Stacking: M:F.23 LMZ.14: 13 residues within 4Å: Chain M: V.112, F.113 Chain N: A.21, F.23, N.24, G.55, A.56, Y.57, E.58, A.80, V.81, V.82, V.92 7 PLIP interactions: 6 interactions with chain N, 1 interactions with chain M Hydrogen bonds: N:N.24, N:A.56, N:Y.57, N:A.80, N:V.82, M:F.113 pi-Stacking: N:F.23 LMZ.15: 12 residues within 4Å: Chain N: V.112, F.113 Chain O: F.23, N.24, G.55, A.56, Y.57, E.58, A.80, V.81, V.82, V.92 10 PLIP interactions: 8 interactions with chain O, 2 interactions with chain N Hydrogen bonds: O:N.24, O:G.55, O:A.56, O:Y.57, O:A.80, O:A.80, O:V.82, N:F.113, N:K.135 pi-Stacking: O:F.23 LMZ.16: 11 residues within 4Å: Chain P: F.23, N.24, G.55, A.56, Y.57, E.58, A.80, V.81, V.82 Chain T: V.112, F.113 8 PLIP interactions: 1 interactions with chain T, 7 interactions with chain P Hydrogen bonds: T:F.113, P:N.24, P:A.56, P:Y.57, P:A.80, P:A.80, P:V.82 pi-Stacking: P:F.23 LMZ.17: 14 residues within 4Å: Chain P: V.112, F.113, K.135 Chain Q: A.21, F.23, N.24, G.55, A.56, Y.57, E.58, A.80, V.81, V.82, V.92 9 PLIP interactions: 6 interactions with chain Q, 3 interactions with chain P Hydrogen bonds: Q:N.24, Q:A.56, Q:Y.57, Q:A.80, Q:V.82, P:F.113, P:K.135, P:K.135 pi-Stacking: Q:F.23 LMZ.18: 14 residues within 4Å: Chain Q: V.112, F.113, K.135 Chain R: A.21, F.23, N.24, G.55, A.56, Y.57, E.58, A.80, V.81, V.82, V.92 9 PLIP interactions: 6 interactions with chain R, 3 interactions with chain Q Hydrogen bonds: R:N.24, R:A.56, R:Y.57, R:A.80, R:V.82, Q:F.113, Q:K.135, Q:K.135 pi-Stacking: R:F.23 LMZ.19: 13 residues within 4Å: Chain R: V.112, F.113 Chain S: A.21, F.23, N.24, G.55, A.56, Y.57, E.58, A.80, V.81, V.82, V.92 9 PLIP interactions: 6 interactions with chain S, 3 interactions with chain R Hydrogen bonds: S:N.24, S:A.56, S:Y.57, S:A.80, S:V.82, R:F.113, R:K.135, R:K.135 pi-Stacking: S:F.23 LMZ.20: 13 residues within 4Å: Chain S: V.112, F.113 Chain T: A.21, F.23, N.24, G.55, A.56, Y.57, E.58, A.80, V.81, V.82, V.92 8 PLIP interactions: 1 interactions with chain S, 7 interactions with chain T Hydrogen bonds: S:F.113, T:N.24, T:A.56, T:Y.57, T:A.80, T:A.80, T:V.82 pi-Stacking: T:F.23

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

2000-07-30

Peptides

PROTEIN (LUMAZINE SYNTHASE): ABCDEFGHIJKLMNOPQRST

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

PROTEIN (LUMAZINE SYNTHASE)

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