SMTL ID : 4oq9.3 (2 other biounits)

Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using non-crystallographic symmetry restraints

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-15-mer

Ligands

15 x U- U: RNA (5'-R(P*UP*U)-3')(Non-covalent)

U-U.1: 11 residues within 4Å: Chain 3: A.8, A.9 Chain 4: U.8, U.9 Chain 8: U.5 Chain A: R.125, R.131 Chain O: N.16, S.17, I.23 Chain U: A.5 11 PLIP interactions: 5 interactions with chain J, 3 interactions with chain A, 3 interactions with chain F Hydrogen bonds: J:N.16, J:N.18, A:T.36, A:T.36, F:V.38, F:V.38, J:N.16, J:N.16, J:N.18, A:T.36 Water bridges: J:V.19, A:V.38, F:V.38, F:V.38, J:V.19, A:V.38 Hydrophobic interactions: A:V.38, F:V.38, F:V.38, J:T.21, A:V.38 U-U.2: 7 residues within 4Å: Chain 3: A.5 Chain 4: U.5 Chain 5: U.8, U.9 Chain B: S.77, R.125, R.131 5 PLIP interactions: 5 interactions with chain O Hydrophobic interactions: O:V.38, O:V.38 Hydrogen bonds: O:T.36, O:T.36, O:T.36 Water bridges: O:V.38, O:T.36, O:V.38 U-U.3: 6 residues within 4Å: Chain 5: U.5 Chain 6: U.8, U.9 Chain C: S.77, R.125, R.131 Protein-ligand interaction information (PLIP) not available U-U.4: 6 residues within 4Å: Chain 6: U.5 Chain 7: U.8, U.9 Chain D: S.77, R.125, R.131 Protein-ligand interaction information (PLIP) not available U-U.5: 11 residues within 4Å: Chain 7: U.5 Chain 8: U.8, U.9 Chain E: S.77, R.125, R.131 Chain F: N.16, S.17, I.23 Chain U: A.8, A.9 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:A.40, E:V.38, E:A.40 Hydrogen bonds: E:V.38, E:V.38, E:R.79, E:R.79, E:V.38, E:S.155 Water bridges: E:V.38, E:A.40, E:A.40, E:A.40, E:R.79, E:R.79, E:S.155, E:V.38, E:A.40, E:A.40, E:S.155 U-U.6: 12 residues within 4Å: Chain 9: U.8, U.9 Chain E: N.16, S.17, I.23 Chain F: S.77, R.125, R.131 Chain T: A.8, A.9 Chain Z: A.5 Chain d: U.5 Protein-ligand interaction information (PLIP) not available U-U.7: 7 residues within 4Å: Chain 9: U.5 Chain G: S.77, R.125, R.131 Chain T: A.5 Chain a: U.8, U.9 Protein-ligand interaction information (PLIP) not available U-U.8: 6 residues within 4Å: Chain H: S.77, R.125, R.131 Chain a: U.5 Chain b: U.8, U.9 Protein-ligand interaction information (PLIP) not available U-U.9: 6 residues within 4Å: Chain I: S.77, R.125, R.131 Chain b: U.5 Chain c: U.8, U.9 Protein-ligand interaction information (PLIP) not available U-U.10: 11 residues within 4Å: Chain J: S.77, R.125, R.131 Chain K: N.16, S.17, I.23 Chain Z: A.8, A.9 Chain c: U.5 Chain d: U.8, U.9 Protein-ligand interaction information (PLIP) not available U-U.11: 13 residues within 4Å: Chain J: N.16, S.17, T.21, I.23 Chain K: S.77, R.125, R.131 Chain P: A.5 Chain Y: A.8, A.9 Chain e: U.8, U.9 Chain i: U.5 Protein-ligand interaction information (PLIP) not available U-U.12: 6 residues within 4Å: Chain L: R.125, R.131 Chain Y: A.5 Chain e: U.5 Chain f: U.8, U.9 Protein-ligand interaction information (PLIP) not available U-U.13: 6 residues within 4Å: Chain M: S.77, R.125, R.131 Chain f: U.5 Chain g: U.8, U.9 Protein-ligand interaction information (PLIP) not available U-U.14: 6 residues within 4Å: Chain N: S.77, R.125, R.131 Chain g: U.5 Chain h: U.8, U.9 Protein-ligand interaction information (PLIP) not available U-U.15: 11 residues within 4Å: Chain A: N.16, S.17, I.23 Chain O: S.77, R.125, R.131 Chain P: A.8, A.9 Chain h: U.5 Chain i: U.8, U.9 Protein-ligand interaction information (PLIP) not available

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

PO4.16: 12 residues within 4Å: Chain A: N.115, N.117 Chain B: N.115, N.117 Chain C: N.115, N.117 Chain D: N.115, N.117 Chain E: N.115, N.117 Ligands: SO4.26, MG.28 11 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 3 interactions with chain E, 2 interactions with chain B, 2 interactions with chain D Hydrogen bonds: A:N.115, A:N.117, C:N.115, C:N.117, E:N.115, E:N.115, E:N.117, B:N.115, B:N.117, D:N.115, D:N.117 PO4.37: 11 residues within 4Å: Chain F: N.115, N.117 Chain G: N.115, N.117 Chain H: N.115, N.117 Chain I: N.115, N.117 Chain J: N.115, N.117 Ligands: MG.32 10 PLIP interactions: 2 interactions with chain F, 2 interactions with chain J, 2 interactions with chain H, 2 interactions with chain G, 2 interactions with chain I Hydrogen bonds: F:N.115, F:N.117, J:N.115, J:N.117, H:N.115, H:N.117, G:N.115, G:N.117, I:N.115, I:N.117 PO4.52: 12 residues within 4Å: Chain K: N.115, N.117 Chain L: N.115, N.117 Chain M: N.115, N.117 Chain N: N.115, N.117 Chain O: N.115, N.117 Ligands: MG.45, SO4.49 13 PLIP interactions: 3 interactions with chain O, 3 interactions with chain L, 2 interactions with chain K, 2 interactions with chain M, 3 interactions with chain N Hydrogen bonds: O:N.115, O:N.115, O:N.117, L:N.115, L:N.115, L:N.117, K:N.115, K:N.117, M:N.115, M:N.117, N:N.115, N:N.115, N:N.117

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

SO4.17: 2 residues within 4Å: Chain A: F.93, R.95 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain B: F.93, R.95 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain C: F.93, R.95 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain D: F.93, R.95 Ligand excluded by PLIP SO4.26: 7 residues within 4Å: Chain A: N.117 Chain B: N.117 Chain C: N.117 Chain D: N.117 Chain E: I.116, N.117 Ligands: PO4.16 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain E: F.93, R.95 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain F: F.93, R.95 Ligand excluded by PLIP SO4.34: 5 residues within 4Å: Chain F: N.117 Chain G: N.117 Chain H: N.117 Chain I: N.117 Chain J: N.117 Ligand excluded by PLIP SO4.35: 2 residues within 4Å: Chain G: F.93, R.95 Ligand excluded by PLIP SO4.38: 2 residues within 4Å: Chain H: F.93, R.95 Ligand excluded by PLIP SO4.40: 2 residues within 4Å: Chain I: F.93, R.95 Ligand excluded by PLIP SO4.42: 2 residues within 4Å: Chain J: F.93, R.95 Ligand excluded by PLIP SO4.44: 2 residues within 4Å: Chain K: F.93, R.95 Ligand excluded by PLIP SO4.47: 2 residues within 4Å: Chain L: F.93, R.95 Ligand excluded by PLIP SO4.49: 8 residues within 4Å: Chain K: I.116, N.117 Chain L: N.117 Chain M: N.117 Chain N: N.117 Chain O: I.116, N.117 Ligands: PO4.52 Ligand excluded by PLIP SO4.50: 2 residues within 4Å: Chain M: F.93, R.95 Ligand excluded by PLIP SO4.53: 2 residues within 4Å: Chain N: F.93, R.95 Ligand excluded by PLIP SO4.55: 2 residues within 4Å: Chain O: F.93, R.95 Ligand excluded by PLIP

17 x NA: SODIUM ION(Non-functional Binders)

NA.18: 4 residues within 4Å: Chain A: R.66, D.68 Chain O: D.68 Ligands: NA.56 Ligand excluded by PLIP NA.20: 1 residues within 4Å: Chain B: D.68 Ligand excluded by PLIP NA.21: 2 residues within 4Å: Chain B: R.66, D.68 Ligand excluded by PLIP NA.23: 2 residues within 4Å: Chain C: R.66, D.68 Ligand excluded by PLIP NA.25: 2 residues within 4Å: Chain D: R.66, D.68 Ligand excluded by PLIP NA.29: 6 residues within 4Å: Chain E: R.66, D.68 Chain F: D.68, S.69 Ligands: NA.30, NA.33 Ligand excluded by PLIP NA.30: 3 residues within 4Å: Chain E: D.68 Chain F: D.68 Ligands: NA.29 Ligand excluded by PLIP NA.33: 5 residues within 4Å: Chain E: D.68, S.69 Chain F: R.66, D.68 Ligands: NA.29 Ligand excluded by PLIP NA.36: 2 residues within 4Å: Chain G: R.66, D.68 Ligand excluded by PLIP NA.39: 2 residues within 4Å: Chain H: R.66, D.68 Ligand excluded by PLIP NA.41: 2 residues within 4Å: Chain I: R.66, D.68 Ligand excluded by PLIP NA.43: 5 residues within 4Å: Chain J: R.66, D.68 Chain K: D.68, S.69 Ligands: NA.46 Ligand excluded by PLIP NA.46: 4 residues within 4Å: Chain J: D.68 Chain K: R.66, D.68 Ligands: NA.43 Ligand excluded by PLIP NA.48: 2 residues within 4Å: Chain L: R.66, D.68 Ligand excluded by PLIP NA.51: 2 residues within 4Å: Chain M: R.66, D.68 Ligand excluded by PLIP NA.54: 2 residues within 4Å: Chain N: R.66, D.68 Ligand excluded by PLIP NA.56: 5 residues within 4Å: Chain A: D.68, S.69 Chain O: R.66, D.68 Ligands: NA.18 Ligand excluded by PLIP

3 x MG: MAGNESIUM ION(Non-covalent)

MG.28: 4 residues within 4Å: Chain A: N.115 Chain D: N.115 Chain E: N.115 Ligands: PO4.16 No protein-ligand interaction detected (PLIP) MG.32: 2 residues within 4Å: Chain F: N.115 Ligands: PO4.37 No protein-ligand interaction detected (PLIP) MG.45: 2 residues within 4Å: Chain L: N.115 Ligands: PO4.52 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Larson, S.B. et al., Satellite tobacco mosaic virus refined to 1.4 angstrom resolution. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-09-10

Peptides

Coat protein: ABCDEFGHIJKLMNO

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

Coat protein

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