SMTL ID : 5bkl.1

Crystallographic structure of the cubic crystal form of STMV (77.9 degree rotation) grown from NaCl

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.94 Å

Oligo State

homo-20-mer

Ligands

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

CL.1: 3 residues within 4Å: Chain B: T.102, Q.132 Chain O: Q.132 Ligand excluded by PLIP CL.2: 7 residues within 4Å: Chain B: P.42, F.43, E.44, A.151, L.152, V.153 Chain C: R.112 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain B: R.39, A.40, I.41, P.42 Ligand excluded by PLIP CL.4: 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 Ligand excluded by PLIP CL.5: 7 residues within 4Å: Chain C: P.86, Y.91, S.92, A.113, N.115, I.116, T.118 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain C: P.86, P.87, V.88, N.89, E.90, I.116 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain C: N.18, V.19 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain C: R.95, E.110, R.112 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain C: Y.28 Ligand excluded by PLIP CL.10: 7 residues within 4Å: Chain C: P.42, F.43, E.44, A.151, L.152, V.153 Chain D: R.112 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain D: A.52, K.97, E.108, E.142, R.144 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain D: S.77, R.79, V.153, S.155 Chain X: U.6 Ligand excluded by PLIP CL.15: 8 residues within 4Å: Chain E: Y.28 Chain F: P.42, F.43, E.44, A.151, L.152, V.153 Chain G: R.112 Ligand excluded by PLIP CL.16: 9 residues within 4Å: Chain F: N.115, N.117 Chain G: N.115, N.117 Chain H: N.115 Chain I: N.115, N.117 Chain J: N.115, N.117 Ligand excluded by PLIP CL.19: 8 residues within 4Å: Chain 2: Y.28 Chain G: P.42, F.43, E.44, A.151, L.152, V.153 Chain H: R.112 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain G: G.26, S.27 Ligand excluded by PLIP CL.22: 5 residues within 4Å: Chain H: A.52, K.97, E.108, E.142, R.144 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain 2: P.33 Chain H: R.95, E.108, E.110 Ligand excluded by PLIP CL.25: 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 Ligand excluded by PLIP CL.26: 8 residues within 4Å: Chain J: Y.28 Chain K: P.42, F.43, E.44, A.151, L.152, V.153 Chain L: R.112 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain L: K.7, P.8 Ligand excluded by PLIP CL.29: 2 residues within 4Å: Chain R: A.1 Chain Y: U.5 Ligand excluded by PLIP CL.30: 4 residues within 4Å: Chain 1: R.39, A.40 Chain 7: A.4, A.5 Ligand excluded by PLIP CL.32: 8 residues within 4Å: Chain 2: P.42, F.43, E.44, A.151, L.152, V.153 Chain 3: R.112 Chain G: Y.28 Ligand excluded by PLIP CL.33: 5 residues within 4Å: Chain 2: R.125, P.127, T.128 Chain G: N.16, S.17 Ligand excluded by PLIP CL.36: 7 residues within 4Å: Chain 3: R.39, A.40, I.41, P.42 Chain D: N.32, P.33, P.35 Ligand excluded by PLIP CL.37: 5 residues within 4Å: Chain 3: N.32, P.35 Chain E: F.109 Chain F: M.22 Chain X: U.4 Ligand excluded by PLIP CL.38: 7 residues within 4Å: Chain 3: P.42, F.43, E.44, A.151, L.152 Chain 4: R.112 Chain D: Y.28 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain 4: I.116, N.117 Ligand excluded by PLIP CL.40: 4 residues within 4Å: Chain 4: R.95, E.108, E.110 Chain D: P.33 Ligand excluded by PLIP CL.41: 4 residues within 4Å: Chain 3: Q.83, L.84 Chain 4: E.90, Y.91 Ligand excluded by PLIP CL.42: 7 residues within 4Å: Chain 4: R.95, L.96, K.97, E.108, E.142, V.143, R.144 Ligand excluded by PLIP CL.43: 7 residues within 4Å: Chain 4: P.42, F.43, E.44, A.151, L.152, V.153 Chain 5: R.112 Ligand excluded by PLIP CL.46: 9 residues within 4Å: Chain 1: N.115, N.117 Chain 2: N.115, N.117 Chain 3: N.115, N.117 Chain 4: N.115 Chain 5: N.115, N.117 Ligand excluded by PLIP CL.47: 1 residues within 4Å: Chain 5: N.159 Ligand excluded by PLIP CL.48: 3 residues within 4Å: Chain 5: R.95, E.108, E.110 Ligand excluded by PLIP CL.49: 2 residues within 4Å: Chain 5: N.16, S.17 Ligand excluded by PLIP CL.50: 7 residues within 4Å: Chain 5: V.47, Q.48, S.49, S.145, N.146, C.147, R.148 Ligand excluded by PLIP CL.52: 2 residues within 4Å: Chain 6: A.1 Chain a: U.4 Ligand excluded by PLIP CL.53: 1 residues within 4Å: Chain b: U.5 Ligand excluded by PLIP

13 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 4 residues within 4Å: Chain E: S.27 Chain F: T.118 Chain G: S.114, N.115 No protein-ligand interaction detected (PLIP) MG.14: 7 residues within 4Å: Chain E: F.70, T.71, S.72, N.159 Chain G: D.104, S.105, T.106 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain E Metal complexes: G:T.106, E:T.71 MG.17: 5 residues within 4Å: Chain F: Q.83, R.119 Chain G: Y.91, F.93, R.112 No protein-ligand interaction detected (PLIP) MG.18: 6 residues within 4Å: Chain F: T.82, F.93, V.94, S.145, C.147, V.150 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:F.93, F:S.145 MG.21: 10 residues within 4Å: Chain G: T.82, L.84, T.85, P.86, S.92, T.118, R.119, A.120, C.147 Chain H: Y.91 4 PLIP interactions: 1 interactions with chain H, 3 interactions with chain G Metal complexes: H:Y.91, G:T.82, G:L.84, G:S.92 MG.24: 9 residues within 4Å: Chain I: T.82, L.84, T.85, P.86, S.92, R.119, A.120, C.147 Chain J: Y.91 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain J Metal complexes: I:T.82, I:L.84, I:S.92, J:Y.91 MG.27: 7 residues within 4Å: Chain K: P.86, Y.91, S.92, A.113, N.115, I.116, T.118 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:S.92, K:I.116 MG.31: 8 residues within 4Å: Chain 1: T.82, L.84, T.85, P.86, S.92, R.119, C.147 Chain 2: Y.91 3 PLIP interactions: 3 interactions with chain 1 Metal complexes: 1:T.82, 1:L.84, 1:S.92 MG.34: 9 residues within 4Å: Chain 2: T.82, L.84, T.85, P.86, S.92, R.119, A.120, C.147 Chain 3: Y.91 4 PLIP interactions: 3 interactions with chain 2, 1 interactions with chain 3 Metal complexes: 2:T.82, 2:L.84, 2:S.92, 3:Y.91 MG.35: 7 residues within 4Å: Chain 2: P.86, Y.91, S.92, A.113, N.115, I.116, T.118 3 PLIP interactions: 3 interactions with chain 2 Metal complexes: 2:S.92, 2:I.116, 2:T.118 MG.44: 7 residues within 4Å: Chain 4: T.82, S.92, F.93, S.145, C.147, Q.149, V.150 2 PLIP interactions: 2 interactions with chain 4 Metal complexes: 4:S.145, 4:C.147 MG.45: 8 residues within 4Å: Chain 4: T.82, L.84, T.85, P.86, S.92, R.119, C.147 Chain 5: Y.91 4 PLIP interactions: 1 interactions with chain 5, 3 interactions with chain 4 Metal complexes: 5:Y.91, 4:T.82, 4:L.84, 4:S.92 MG.51: 9 residues within 4Å: Chain 1: Y.91 Chain 5: T.82, L.84, T.85, P.86, S.92, R.119, A.120, C.147 4 PLIP interactions: 3 interactions with chain 5, 1 interactions with chain 1 Metal complexes: 5:T.82, 5:L.84, 5:S.92, 1: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: ABCDEFGHIJKLMNO12345

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

1
GG

2
HH

3
II

4
JJ

5
KK

Coat protein

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