SMTL ID : 3pdm.1 (2 other biounits)

Hibiscus Latent Singapore virus

Coordinates

PDB Format

Method

FIBER DIFFRACTION 3.50 Å

Oligo State

homo-49-mer

Ligands

49 x G- A- A: RNA (5'-R(P*GP*AP*A)-3')(Non-covalent)

G-A-A.1: 13 residues within 4Å: Chain A: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain B: V.119 Ligands: G-A-A.2 Protein-ligand interaction information (PLIP) not available G-A-A.2: 16 residues within 4Å: Chain A: T.89, R.113 Chain B: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain C: V.119 Ligands: G-A-A.1, G-A-A.3 Protein-ligand interaction information (PLIP) not available G-A-A.3: 16 residues within 4Å: Chain B: T.89, R.113 Chain C: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain D: V.119 Ligands: G-A-A.2, G-A-A.4 Protein-ligand interaction information (PLIP) not available G-A-A.4: 16 residues within 4Å: Chain C: T.89, R.113 Chain D: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain E: V.119 Ligands: G-A-A.3, G-A-A.5 Protein-ligand interaction information (PLIP) not available G-A-A.5: 16 residues within 4Å: Chain D: T.89, R.113 Chain E: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain F: V.119 Ligands: G-A-A.4, G-A-A.6 Protein-ligand interaction information (PLIP) not available G-A-A.6: 16 residues within 4Å: Chain E: T.89, R.113 Chain F: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain G: V.119 Ligands: G-A-A.5, G-A-A.7 Protein-ligand interaction information (PLIP) not available G-A-A.7: 16 residues within 4Å: Chain F: T.89, R.113 Chain G: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain H: V.119 Ligands: G-A-A.6, G-A-A.8 Protein-ligand interaction information (PLIP) not available G-A-A.8: 16 residues within 4Å: Chain G: T.89, R.113 Chain H: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain I: V.119 Ligands: G-A-A.7, G-A-A.9 Protein-ligand interaction information (PLIP) not available G-A-A.9: 16 residues within 4Å: Chain H: T.89, R.113 Chain I: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain J: V.119 Ligands: G-A-A.8, G-A-A.10 Protein-ligand interaction information (PLIP) not available G-A-A.10: 16 residues within 4Å: Chain I: T.89, R.113 Chain J: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain K: V.119 Ligands: G-A-A.9, G-A-A.11 Protein-ligand interaction information (PLIP) not available G-A-A.11: 16 residues within 4Å: Chain J: T.89, R.113 Chain K: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain L: V.119 Ligands: G-A-A.10, G-A-A.12 Protein-ligand interaction information (PLIP) not available G-A-A.12: 16 residues within 4Å: Chain K: T.89, R.113 Chain L: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain M: V.119 Ligands: G-A-A.11, G-A-A.13 Protein-ligand interaction information (PLIP) not available G-A-A.13: 16 residues within 4Å: Chain L: T.89, R.113 Chain M: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain N: V.119 Ligands: G-A-A.12, G-A-A.14 Protein-ligand interaction information (PLIP) not available G-A-A.14: 16 residues within 4Å: Chain M: T.89, R.113 Chain N: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain O: V.119 Ligands: G-A-A.13, G-A-A.15 Protein-ligand interaction information (PLIP) not available G-A-A.15: 16 residues within 4Å: Chain N: T.89, R.113 Chain O: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain P: V.119 Ligands: G-A-A.14, G-A-A.16 Protein-ligand interaction information (PLIP) not available G-A-A.16: 16 residues within 4Å: Chain O: T.89, R.113 Chain P: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain Q: V.119 Ligands: G-A-A.15, G-A-A.17 Protein-ligand interaction information (PLIP) not available G-A-A.17: 23 residues within 4Å: Chain A: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Chain P: T.89, R.113 Chain Q: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain R: V.119 Ligands: G-A-A.16, G-A-A.18 Protein-ligand interaction information (PLIP) not available G-A-A.18: 24 residues within 4Å: Chain A: R.92 Chain B: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Chain Q: T.89, R.113 Chain R: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain S: V.119 Ligands: G-A-A.17, G-A-A.19 Protein-ligand interaction information (PLIP) not available G-A-A.19: 24 residues within 4Å: Chain B: R.92 Chain C: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Chain R: T.89, R.113 Chain S: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain T: V.119 Ligands: G-A-A.18, G-A-A.20 Protein-ligand interaction information (PLIP) not available G-A-A.20: 24 residues within 4Å: Chain C: R.92 Chain D: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Chain S: T.89, R.113 Chain T: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain U: V.119 Ligands: G-A-A.19, G-A-A.21 Protein-ligand interaction information (PLIP) not available G-A-A.21: 24 residues within 4Å: Chain D: R.92 Chain E: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Chain T: T.89, R.113 Chain U: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain V: V.119 Ligands: G-A-A.20, G-A-A.22 Protein-ligand interaction information (PLIP) not available G-A-A.22: 24 residues within 4Å: Chain E: R.92 Chain F: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Chain U: T.89, R.113 Chain V: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain W: V.119 Ligands: G-A-A.21, G-A-A.23 Protein-ligand interaction information (PLIP) not available G-A-A.23: 24 residues within 4Å: Chain F: R.92 Chain G: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Chain V: T.89, R.113 Chain W: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain X: V.119 Ligands: G-A-A.22, G-A-A.24 Protein-ligand interaction information (PLIP) not available G-A-A.24: 24 residues within 4Å: Chain G: R.92 Chain H: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Chain W: T.89, R.113 Chain X: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain Y: V.119 Ligands: G-A-A.23, G-A-A.25 Protein-ligand interaction information (PLIP) not available G-A-A.25: 24 residues within 4Å: Chain H: R.92 Chain I: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Chain X: T.89, R.113 Chain Y: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain Z: V.119 Ligands: G-A-A.24, G-A-A.26 Protein-ligand interaction information (PLIP) not available G-A-A.26: 24 residues within 4Å: Chain 0: V.119 Chain I: R.92 Chain J: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Chain Y: T.89, R.113 Chain Z: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Ligands: G-A-A.25, G-A-A.27 Protein-ligand interaction information (PLIP) not available G-A-A.27: 24 residues within 4Å: Chain 0: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain 1: V.119 Chain J: R.92 Chain K: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Chain Z: T.89, R.113 Ligands: G-A-A.26, G-A-A.28 Protein-ligand interaction information (PLIP) not available G-A-A.28: 24 residues within 4Å: Chain 0: T.89, R.113 Chain 1: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain 2: V.119 Chain K: R.92 Chain L: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Ligands: G-A-A.27, G-A-A.29 Protein-ligand interaction information (PLIP) not available G-A-A.29: 24 residues within 4Å: Chain 1: T.89, R.113 Chain 2: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain 3: V.119 Chain L: R.92 Chain M: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Ligands: G-A-A.28, G-A-A.30 Protein-ligand interaction information (PLIP) not available G-A-A.30: 24 residues within 4Å: Chain 2: T.89, R.113 Chain 3: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain 4: V.119 Chain M: R.92 Chain N: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Ligands: G-A-A.29, G-A-A.31 Protein-ligand interaction information (PLIP) not available G-A-A.31: 24 residues within 4Å: Chain 3: T.89, R.113 Chain 4: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain 5: V.119 Chain N: R.92 Chain O: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Ligands: G-A-A.30, G-A-A.32 Protein-ligand interaction information (PLIP) not available G-A-A.32: 24 residues within 4Å: Chain 4: T.89, R.113 Chain 5: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain 6: V.119 Chain O: R.92 Chain P: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Ligands: G-A-A.31, G-A-A.33 Protein-ligand interaction information (PLIP) not available G-A-A.33: 24 residues within 4Å: Chain 5: T.89, R.113 Chain 6: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain 7: V.119 Chain P: R.92 Chain Q: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Ligands: G-A-A.32, G-A-A.34 Protein-ligand interaction information (PLIP) not available G-A-A.34: 24 residues within 4Å: Chain 6: T.89, R.113 Chain 7: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain 8: V.119 Chain Q: R.92 Chain R: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Ligands: G-A-A.33, G-A-A.35 Protein-ligand interaction information (PLIP) not available G-A-A.35: 24 residues within 4Å: Chain 7: T.89, R.113 Chain 8: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain 9: V.119 Chain R: R.92 Chain S: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Ligands: G-A-A.34, G-A-A.36 Protein-ligand interaction information (PLIP) not available G-A-A.36: 24 residues within 4Å: Chain 8: T.89, R.113 Chain 9: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain S: R.92 Chain T: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Ligands: G-A-A.35, G-A-A.37 Chain a: V.119 Protein-ligand interaction information (PLIP) not available G-A-A.37: 24 residues within 4Å: Chain 9: T.89, R.113 Chain T: R.92 Chain U: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Ligands: G-A-A.36, G-A-A.38 Chain a: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain b: V.119 Protein-ligand interaction information (PLIP) not available G-A-A.38: 24 residues within 4Å: Chain U: R.92 Chain V: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Ligands: G-A-A.37, G-A-A.39 Chain a: T.89, R.113 Chain b: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain c: V.119 Protein-ligand interaction information (PLIP) not available G-A-A.39: 24 residues within 4Å: Chain V: R.92 Chain W: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Ligands: G-A-A.38, G-A-A.40 Chain b: T.89, R.113 Chain c: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain d: V.119 Protein-ligand interaction information (PLIP) not available G-A-A.40: 24 residues within 4Å: Chain W: R.92 Chain X: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Ligands: G-A-A.39, G-A-A.41 Chain c: T.89, R.113 Chain d: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain e: V.119 Protein-ligand interaction information (PLIP) not available G-A-A.41: 24 residues within 4Å: Chain X: R.92 Chain Y: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Ligands: G-A-A.40, G-A-A.42 Chain d: T.89, R.113 Chain e: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain f: V.119 Protein-ligand interaction information (PLIP) not available G-A-A.42: 24 residues within 4Å: Chain Y: R.92 Chain Z: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Ligands: G-A-A.41, G-A-A.43 Chain e: T.89, R.113 Chain f: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain g: V.119 Protein-ligand interaction information (PLIP) not available G-A-A.43: 24 residues within 4Å: Chain 0: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Chain Z: R.92 Ligands: G-A-A.42, G-A-A.44 Chain f: T.89, R.113 Chain g: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain h: V.119 Protein-ligand interaction information (PLIP) not available G-A-A.44: 24 residues within 4Å: Chain 0: R.92 Chain 1: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Ligands: G-A-A.43, G-A-A.45 Chain g: T.89, R.113 Chain h: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain i: V.119 Protein-ligand interaction information (PLIP) not available G-A-A.45: 24 residues within 4Å: Chain 1: R.92 Chain 2: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Ligands: G-A-A.44, G-A-A.46 Chain h: T.89, R.113 Chain i: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain j: V.119 Protein-ligand interaction information (PLIP) not available G-A-A.46: 24 residues within 4Å: Chain 2: R.92 Chain 3: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Ligands: G-A-A.45, G-A-A.47 Chain i: T.89, R.113 Chain j: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain k: V.119 Protein-ligand interaction information (PLIP) not available G-A-A.47: 24 residues within 4Å: Chain 3: R.92 Chain 4: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Ligands: G-A-A.46, G-A-A.48 Chain j: T.89, R.113 Chain k: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain l: V.119 Protein-ligand interaction information (PLIP) not available G-A-A.48: 24 residues within 4Å: Chain 4: R.92 Chain 5: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Ligands: G-A-A.47, G-A-A.49 Chain k: T.89, R.113 Chain l: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Chain m: V.119 Protein-ligand interaction information (PLIP) not available G-A-A.49: 22 residues within 4Å: Chain 5: R.92 Chain 6: N.33, S.34, T.37, Q.38, A.39, G.40, I.94 Ligands: G-A-A.48 Chain l: T.89, R.113 Chain m: A.86, T.89, R.113, D.115, D.116, A.117, T.118, V.119, A.120, K.123, N.127 Protein-ligand interaction information (PLIP) not available

Links

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Citation

Tewary, S.K. et al., Structure of Hibiscus latent Singapore virus by fiber diffraction: A non-conserved His122 contributes to coat protein stability. J.Mol.Biol. (2010)

Release Date

2011-01-12

Peptides

Coat protein: ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789abcdefghijklm

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

B
P

C
P

D
P

E
P

F
P

G
P

H
P

I
P

J
P

K
P

L
P

M
P

N
P

O
P

P
P

Q
P

R
P

S
P

T
P

U
P

V
P

W
P

X
P

Y
P

Z
P

0
P

1
P

2
P

3
P

4
P

5
P

6
P

7
P

8
P

9
P

a
P

b
P

c
P

d
P

e
P

f
P

g
P

h
P

i
P

j
P

k
P

l
P

m
P

Coat protein

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