SMTL ID : 7m3t.1

Crystallographic structure of a cubic crystal of STMV (80.7 degree rotation about 111) grown from chloride

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-18-1-1-mer

Ligands

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

U-U-U-U.1: 19 residues within 4Å: Chain E: S.17, V.19, T.21, M.22, R.24 Chain J: V.38, R.39, A.40, R.79, S.155 Chain K: P.29, K.30, V.31, P.35, T.36, V.38 Chain U: A.2, A.3, A.4 Protein-ligand interaction information (PLIP) not available U-U-U-U.2: 10 residues within 4Å: Chain 0: R.125 Chain 4: V.38, S.77, R.79, R.125, R.131 Chain 8: A.6, A.8, A.9 Ligands: CL.29 Protein-ligand interaction information (PLIP) not available

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

PO4.3: 10 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 10 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B, 2 interactions with chain E, 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: D:N.115, D:N.117, B:N.115, B:N.117, E:N.115, E:N.117, A:N.115, A:N.117, C:N.115, C:N.117 PO4.8: 9 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.117 9 PLIP interactions: 2 interactions with chain F, 1 interactions with chain J, 2 interactions with chain H, 2 interactions with chain I, 2 interactions with chain G Hydrogen bonds: F:N.115, F:N.117, J:N.117, H:N.115, H:N.117, I:N.115, I:N.115, G:N.115, G:N.117 PO4.10: 4 residues within 4Å: Chain H: R.66, T.67, D.68, S.69 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:D.68, H:D.68, H:S.69 PO4.11: 10 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 11 PLIP interactions: 2 interactions with chain L, 2 interactions with chain K, 2 interactions with chain O, 3 interactions with chain M, 2 interactions with chain N Hydrogen bonds: L:N.115, L:N.117, K:N.115, K:N.117, O:N.115, O:N.117, M:N.115, M:N.115, M:N.117, N:N.115, N:N.117 PO4.15: 3 residues within 4Å: Chain 2: R.79, S.155 Chain Q: A.5 4 PLIP interactions: 4 interactions with chain 2 Hydrogen bonds: 2:S.155, 2:S.155 Water bridges: 2:R.79 Salt bridges: 2:R.79 PO4.17: 9 residues within 4Å: Chain 0: N.115, N.117 Chain 1: N.115, N.117 Chain 2: N.115, N.117 Chain 3: N.115, N.117 Chain 4: N.117 12 PLIP interactions: 3 interactions with chain 0, 2 interactions with chain 1, 2 interactions with chain 4, 3 interactions with chain 3, 2 interactions with chain 2 Hydrogen bonds: 0:N.115, 0:N.115, 0:N.117, 1:N.115, 1:N.117, 4:N.115, 4:N.117, 3:N.115, 3:N.115, 3:N.117, 2:N.115, 2:N.117 PO4.28: 1 residues within 4Å: Chain a: U.1 No protein-ligand interaction detected (PLIP)

15 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.7: 7 residues within 4Å: Chain 1: Y.28 Chain G: P.42, F.43, E.44, A.151, L.152 Chain H: R.112 Ligand excluded by PLIP CL.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain F: V.38 Chain R: A.4, A.5 Ligand excluded by PLIP CL.18: 7 residues within 4Å: Chain 1: F.70, T.71, S.72, N.159 Chain H: D.104, S.105, T.106 Ligand excluded by PLIP CL.22: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.24: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.25: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.26: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.29: 1 residues within 4Å: Ligands: U-U-U-U.2 Ligand excluded by PLIP CL.30: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

6 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 6 residues within 4Å: Chain H: P.86, S.92, A.113, N.115, I.116, T.118 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:S.92, H:I.116, H:T.118 MG.12: 7 residues within 4Å: Chain L: T.82, L.84, S.92, T.118, R.119, C.147 Chain M: Y.91 3 PLIP interactions: 1 interactions with chain M, 2 interactions with chain L Metal complexes: M:Y.91, L:T.82, L:S.92 MG.19: 4 residues within 4Å: Chain 2: T.82, Q.83, L.84 Chain 3: Y.91 3 PLIP interactions: 2 interactions with chain 2, 1 Ligand-Water interactions Metal complexes: 2:T.82, 2:L.84, H2O.34 MG.20: 2 residues within 4Å: Chain 3: T.118 Chain 4: N.115 1 PLIP interactions: 1 interactions with chain 3 Metal complexes: 3:T.118 MG.21: 5 residues within 4Å: Chain 3: T.82, L.84, S.92, C.147 Chain 4: Y.91 4 PLIP interactions: 3 interactions with chain 3, 1 interactions with chain 4 Metal complexes: 3:T.82, 3:L.84, 3:S.92, 4:Y.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McPherson, A., Structures of additional crystal forms of Satellite tobacco mosaic virus grown from a variety of salts. Acta Crystallogr.,Sect.F (2021)

Release Date

2021-12-15

Peptides

Coat protein: ABCDEFHIJKLMO01234
Coat protein: G
Coat protein: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

H
H

I
I

J
J

K
K

L
L

M
M

O
O

0
GG

1
HH

2
II

3
JJ

4
KK

G
G

N
N

Coat protein

Coat protein

Coat protein

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