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

SYNTHASE/RIBOFLAVIN SYNTHASE COMPLEX OF BACILLUS SUBTILIS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-30-mer

Ligands

30 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 Ligand excluded by PLIP PO4.3: 5 residues within 4Å: Chain A: R.127 Chain B: G.84, A.85, T.86, H.88 Ligand excluded by PLIP PO4.5: 5 residues within 4Å: Chain B: R.127 Chain C: G.84, A.85, T.86, H.88 Ligand excluded by PLIP PO4.7: 5 residues within 4Å: Chain C: R.127 Chain D: G.84, A.85, T.86, H.88 Ligand excluded by PLIP PO4.9: 5 residues within 4Å: Chain D: R.127 Chain E: G.84, A.85, T.86, H.88 Ligand excluded by PLIP PO4.11: 5 residues within 4Å: Chain F: G.84, A.85, T.86, H.88 Chain J: R.127 Ligand excluded by PLIP PO4.13: 5 residues within 4Å: Chain F: R.127 Chain G: G.84, A.85, T.86, H.88 Ligand excluded by PLIP PO4.15: 5 residues within 4Å: Chain G: R.127 Chain H: G.84, A.85, T.86, H.88 Ligand excluded by PLIP PO4.17: 5 residues within 4Å: Chain H: R.127 Chain I: G.84, A.85, T.86, H.88 Ligand excluded by PLIP PO4.19: 5 residues within 4Å: Chain I: R.127 Chain J: G.84, A.85, T.86, H.88 Ligand excluded by PLIP PO4.21: 5 residues within 4Å: Chain K: G.84, A.85, T.86, H.88 Chain O: R.127 Ligand excluded by PLIP PO4.23: 5 residues within 4Å: Chain K: R.127 Chain L: G.84, A.85, T.86, H.88 Ligand excluded by PLIP PO4.25: 5 residues within 4Å: Chain L: R.127 Chain M: G.84, A.85, T.86, H.88 Ligand excluded by PLIP PO4.27: 5 residues within 4Å: Chain M: R.127 Chain N: G.84, A.85, T.86, H.88 Ligand excluded by PLIP PO4.29: 5 residues within 4Å: Chain N: R.127 Chain O: G.84, A.85, T.86, H.88 Ligand excluded by PLIP PO4.31: 5 residues within 4Å: Chain P: G.84, A.85, T.86, H.88 Chain T: R.127 Ligand excluded by PLIP PO4.33: 5 residues within 4Å: Chain P: R.127 Chain Q: G.84, A.85, T.86, H.88 Ligand excluded by PLIP PO4.35: 5 residues within 4Å: Chain Q: R.127 Chain R: G.84, A.85, T.86, H.88 Ligand excluded by PLIP PO4.37: 5 residues within 4Å: Chain R: R.127 Chain S: G.84, A.85, T.86, H.88 Ligand excluded by PLIP PO4.39: 5 residues within 4Å: Chain S: R.127 Chain T: G.84, A.85, T.86, H.88 Ligand excluded by PLIP PO4.41: 5 residues within 4Å: Chain U: G.84, A.85, T.86, H.88 Chain Y: R.127 Ligand excluded by PLIP PO4.43: 5 residues within 4Å: Chain U: R.127 Chain V: G.84, A.85, T.86, H.88 Ligand excluded by PLIP PO4.45: 5 residues within 4Å: Chain V: R.127 Chain W: G.84, A.85, T.86, H.88 Ligand excluded by PLIP PO4.47: 5 residues within 4Å: Chain W: R.127 Chain X: G.84, A.85, T.86, H.88 Ligand excluded by PLIP PO4.49: 5 residues within 4Å: Chain X: R.127 Chain Y: G.84, A.85, T.86, H.88 Ligand excluded by PLIP PO4.51: 5 residues within 4Å: Chain 3: R.127 Chain Z: G.84, A.85, T.86, H.88 Ligand excluded by PLIP PO4.53: 5 residues within 4Å: Chain 0: G.84, A.85, T.86, H.88 Chain Z: R.127 Ligand excluded by PLIP PO4.55: 5 residues within 4Å: Chain 0: R.127 Chain 1: G.84, A.85, T.86, H.88 Ligand excluded by PLIP PO4.57: 5 residues within 4Å: Chain 1: R.127 Chain 2: G.84, A.85, T.86, H.88 Ligand excluded by PLIP PO4.59: 5 residues within 4Å: Chain 2: R.127 Chain 3: G.84, A.85, T.86, H.88 Ligand excluded by PLIP

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

INI.2: 15 residues within 4Å: Chain A: F.22, N.23, P.54, 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: 15 residues within 4Å: Chain A: I.112, F.113, K.135 Chain B: F.22, N.23, P.54, 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: 15 residues within 4Å: Chain B: I.112, F.113, K.135 Chain C: F.22, N.23, P.54, 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 C, 2 interactions with chain B Hydrogen bonds: C:N.23, C:A.56, C:F.57, C:T.80, C:I.82, B:F.113, B:K.135 pi-Stacking: C:F.22 INI.8: 15 residues within 4Å: Chain C: I.112, F.113, K.135 Chain D: F.22, N.23, P.54, 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: 15 residues within 4Å: Chain D: I.112, F.113, K.135 Chain E: F.22, N.23, P.54, 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 INI.12: 15 residues within 4Å: Chain F: F.22, N.23, P.54, G.55, A.56, F.57, E.58, T.80, V.81, I.82, H.88, V.92 Chain J: I.112, F.113, K.135 8 PLIP interactions: 6 interactions with chain F, 2 interactions with chain J Hydrogen bonds: F:N.23, F:A.56, F:F.57, F:T.80, F:I.82, J:F.113, J:K.135 pi-Stacking: F:F.22 INI.14: 15 residues within 4Å: Chain F: I.112, F.113, K.135 Chain G: F.22, N.23, P.54, 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 G, 2 interactions with chain F Hydrogen bonds: G:N.23, G:A.56, G:F.57, G:T.80, G:I.82, F:F.113, F:K.135 pi-Stacking: G:F.22 INI.16: 15 residues within 4Å: Chain G: I.112, F.113, K.135 Chain H: F.22, N.23, P.54, 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 G, 6 interactions with chain H Hydrogen bonds: G:F.113, G:K.135, H:N.23, H:A.56, H:F.57, H:T.80, H:I.82 pi-Stacking: H:F.22 INI.18: 15 residues within 4Å: Chain H: I.112, F.113, K.135 Chain I: F.22, N.23, P.54, 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 I, 2 interactions with chain H Hydrogen bonds: I:N.23, I:A.56, I:F.57, I:T.80, I:I.82, H:F.113, H:K.135 pi-Stacking: I:F.22 INI.20: 15 residues within 4Å: Chain I: I.112, F.113, K.135 Chain J: F.22, N.23, P.54, 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 J, 2 interactions with chain I Hydrogen bonds: J:N.23, J:A.56, J:F.57, J:T.80, J:I.82, I:F.113, I:K.135 pi-Stacking: J:F.22 INI.22: 15 residues within 4Å: Chain K: F.22, N.23, P.54, G.55, A.56, F.57, E.58, T.80, V.81, I.82, H.88, V.92 Chain O: I.112, F.113, K.135 7 PLIP interactions: 6 interactions with chain K, 1 interactions with chain O Hydrogen bonds: K:N.23, K:A.56, K:F.57, K:T.80, K:I.82, O:F.113 pi-Stacking: K:F.22 INI.24: 15 residues within 4Å: Chain K: I.112, F.113, K.135 Chain L: F.22, N.23, P.54, 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 K, 6 interactions with chain L Hydrogen bonds: K:F.113, K:K.135, L:N.23, L:A.56, L:F.57, L:T.80, L:I.82 pi-Stacking: L:F.22 INI.26: 15 residues within 4Å: Chain L: I.112, F.113, K.135 Chain M: F.22, N.23, P.54, 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 L, 6 interactions with chain M Hydrogen bonds: L:F.113, L:K.135, M:N.23, M:A.56, M:F.57, M:T.80, M:I.82 pi-Stacking: M:F.22 INI.28: 15 residues within 4Å: Chain M: I.112, F.113, K.135 Chain N: F.22, N.23, P.54, 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 N, 2 interactions with chain M Hydrogen bonds: N:N.23, N:A.56, N:F.57, N:T.80, N:I.82, M:F.113, M:K.135 pi-Stacking: N:F.22 INI.30: 15 residues within 4Å: Chain N: I.112, F.113, K.135 Chain O: F.22, N.23, P.54, 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 O, 2 interactions with chain N Hydrogen bonds: O:N.23, O:A.56, O:F.57, O:T.80, O:I.82, N:F.113, N:K.135 pi-Stacking: O:F.22 INI.32: 15 residues within 4Å: Chain P: F.22, N.23, P.54, G.55, A.56, F.57, E.58, T.80, V.81, I.82, H.88, V.92 Chain T: I.112, F.113, K.135 8 PLIP interactions: 6 interactions with chain P, 2 interactions with chain T Hydrogen bonds: P:N.23, P:A.56, P:F.57, P:T.80, P:I.82, T:F.113, T:K.135 pi-Stacking: P:F.22 INI.34: 15 residues within 4Å: Chain P: I.112, F.113, K.135 Chain Q: F.22, N.23, P.54, 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 Q, 2 interactions with chain P Hydrogen bonds: Q:N.23, Q:A.56, Q:F.57, Q:T.80, Q:I.82, P:F.113, P:K.135 pi-Stacking: Q:F.22 INI.36: 15 residues within 4Å: Chain Q: I.112, F.113, K.135 Chain R: F.22, N.23, P.54, 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 R, 2 interactions with chain Q Hydrogen bonds: R:N.23, R:A.56, R:F.57, R:T.80, R:I.82, Q:F.113, Q:K.135 pi-Stacking: R:F.22 INI.38: 15 residues within 4Å: Chain R: I.112, F.113, K.135 Chain S: F.22, N.23, P.54, 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 S, 2 interactions with chain R Hydrogen bonds: S:N.23, S:A.56, S:F.57, S:T.80, S:I.82, R:F.113, R:K.135 pi-Stacking: S:F.22 INI.40: 15 residues within 4Å: Chain S: I.112, F.113, K.135 Chain T: F.22, N.23, P.54, 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 T, 2 interactions with chain S Hydrogen bonds: T:N.23, T:A.56, T:F.57, T:T.80, T:I.82, S:F.113, S:K.135 pi-Stacking: T:F.22 INI.42: 15 residues within 4Å: Chain U: F.22, N.23, P.54, G.55, A.56, F.57, E.58, T.80, V.81, I.82, H.88, V.92 Chain Y: I.112, F.113, K.135 8 PLIP interactions: 6 interactions with chain U, 2 interactions with chain Y Hydrogen bonds: U:N.23, U:A.56, U:F.57, U:T.80, U:I.82, Y:F.113, Y:K.135 pi-Stacking: U:F.22 INI.44: 15 residues within 4Å: Chain U: I.112, F.113, K.135 Chain V: F.22, N.23, P.54, 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 V, 2 interactions with chain U Hydrogen bonds: V:N.23, V:A.56, V:F.57, V:T.80, V:I.82, U:F.113, U:K.135 pi-Stacking: V:F.22 INI.46: 15 residues within 4Å: Chain V: I.112, F.113, K.135 Chain W: F.22, N.23, P.54, G.55, A.56, F.57, E.58, T.80, V.81, I.82, H.88, V.92 9 PLIP interactions: 6 interactions with chain W, 3 interactions with chain V Hydrogen bonds: W:N.23, W:A.56, W:F.57, W:T.80, W:I.82, V:F.113, V:K.135, V:K.135 pi-Stacking: W:F.22 INI.48: 15 residues within 4Å: Chain W: I.112, F.113, K.135 Chain X: F.22, N.23, P.54, 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 W, 6 interactions with chain X Hydrogen bonds: W:F.113, W:K.135, X:N.23, X:A.56, X:F.57, X:T.80, X:I.82 pi-Stacking: X:F.22 INI.50: 15 residues within 4Å: Chain X: I.112, F.113, K.135 Chain Y: F.22, N.23, P.54, 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 Y, 2 interactions with chain X Hydrogen bonds: Y:N.23, Y:A.56, Y:F.57, Y:T.80, Y:I.82, X:F.113, X:K.135 pi-Stacking: Y:F.22 INI.52: 15 residues within 4Å: Chain 3: I.112, F.113, K.135 Chain Z: F.22, N.23, P.54, 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 Z, 2 interactions with chain 3 Hydrogen bonds: Z:N.23, Z:A.56, Z:F.57, Z:T.80, Z:I.82, 3:F.113, 3:K.135 pi-Stacking: Z:F.22 INI.54: 15 residues within 4Å: Chain 0: F.22, N.23, P.54, G.55, A.56, F.57, E.58, T.80, V.81, I.82, H.88, V.92 Chain Z: I.112, F.113, K.135 8 PLIP interactions: 6 interactions with chain 0, 2 interactions with chain Z Hydrogen bonds: 0:N.23, 0:A.56, 0:F.57, 0:T.80, 0:I.82, Z:F.113, Z:K.135 pi-Stacking: 0:F.22 INI.56: 15 residues within 4Å: Chain 0: I.112, F.113, K.135 Chain 1: F.22, N.23, P.54, G.55, A.56, F.57, E.58, T.80, V.81, I.82, H.88, V.92 7 PLIP interactions: 6 interactions with chain 1, 1 interactions with chain 0 Hydrogen bonds: 1:N.23, 1:A.56, 1:F.57, 1:T.80, 1:I.82, 0:F.113 pi-Stacking: 1:F.22 INI.58: 15 residues within 4Å: Chain 1: I.112, F.113, K.135 Chain 2: F.22, N.23, P.54, 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 2, 2 interactions with chain 1 Hydrogen bonds: 2:N.23, 2:A.56, 2:F.57, 2:T.80, 2:I.82, 1:F.113, 1:K.135 pi-Stacking: 2:F.22 INI.60: 15 residues within 4Å: Chain 2: I.112, F.113, K.135 Chain 3: F.22, N.23, P.54, 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 3, 2 interactions with chain 2 Hydrogen bonds: 3:N.23, 3:A.56, 3:F.57, 3:T.80, 3:I.82, 2:F.113, 2:K.135 pi-Stacking: 3:F.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ritsert, K. et al., Studies on the lumazine synthase/riboflavin synthase complex of Bacillus subtilis: crystal structure analysis of reconstituted, icosahedral beta-subunit capsids with bound substrate analogue inhibitor at 2.4 A resolution. J.Mol.Biol. (1995)

Release Date

1996-12-07

Peptides

RIBOFLAVIN SYNTHASE: ABCDEFGHIJKLMNOPQRSTUVWXYZ0123

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

U
U

V
V

W
W

X
X

Y
Y

Z
Z

0
1

1
2

2
3

3
4

RIBOFLAVIN SYNTHASE

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