SMTL ID : 6bvf.3 (3 other biounits)

Cryo-EM Structure of Hepatitis B virus T=4 capsid in complex with the fluorescent allosteric modulator HAP-TAMRA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-24-mer

Ligands

12 x E9D: Heteroaryldihydropyrimidine tetramethylrodamine(Non-covalent)

E9D.1: 20 residues within 4Å: Chain B: F.23, P.25, D.29, L.30, T.33, W.102, I.105, S.106, F.110, Y.118, I.139, L.140 Chain C: V.124, R.127, T.128, P.129, Y.132, P.134 Ligands: E9D.5, E9D.6 12 PLIP interactions: 5 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: C:V.124, C:T.128, C:P.129, C:Y.132, C:P.134, B:F.23, B:P.25, B:T.33, B:I.105, B:I.139, B:L.140 Halogen bonds: B:D.29 E9D.2: 20 residues within 4Å: Chain C: F.23, P.25, L.30, T.33, W.102, I.105, S.106, F.110, Y.118, L.140 Chain J: N.136 Chain P: V.124, W.125, T.128, P.129, Y.132, P.134, N.136, I.139 Ligands: E9D.5 5 PLIP interactions: 1 interactions with chain P, 4 interactions with chain C Hydrophobic interactions: P:T.128, C:F.23, C:P.25, C:I.105 Hydrogen bonds: C:Y.118 E9D.3: 20 residues within 4Å: Chain F: F.23, P.25, D.29, L.30, T.33, W.102, I.105, S.106, F.110, Y.118, I.139, L.140 Chain G: V.124, R.127, T.128, P.129, Y.132, P.134 Ligands: E9D.9, E9D.10 12 PLIP interactions: 5 interactions with chain G, 7 interactions with chain F Hydrophobic interactions: G:V.124, G:T.128, G:P.129, G:Y.132, G:P.134, F:F.23, F:P.25, F:T.33, F:I.105, F:I.139, F:L.140 Halogen bonds: F:D.29 E9D.4: 12 residues within 4Å: Chain G: F.23, P.25, L.30, T.33, W.102, I.105, S.106, F.110, Y.118, L.140 Chain R: N.136 Ligands: E9D.9 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:F.23, G:P.25, G:I.105 Hydrogen bonds: G:Y.118 E9D.5: 20 residues within 4Å: Chain J: F.23, P.25, D.29, L.30, T.33, W.102, I.105, S.106, F.110, Y.118, I.139, L.140 Chain K: V.124, R.127, T.128, P.129, Y.132, P.134 Ligands: E9D.1, E9D.2 12 PLIP interactions: 5 interactions with chain K, 7 interactions with chain J Hydrophobic interactions: K:V.124, K:T.128, K:P.129, K:Y.132, K:P.134, J:F.23, J:P.25, J:T.33, J:I.105, J:I.139, J:L.140 Halogen bonds: J:D.29 E9D.6: 12 residues within 4Å: Chain B: N.136 Chain K: F.23, P.25, L.30, T.33, W.102, I.105, S.106, F.110, Y.118, L.140 Ligands: E9D.1 3 PLIP interactions: 3 interactions with chain K Hydrophobic interactions: K:F.23, K:P.25, K:I.105 E9D.7: 20 residues within 4Å: Chain N: F.23, P.25, D.29, L.30, T.33, W.102, I.105, S.106, F.110, Y.118, I.139, L.140 Chain O: V.124, R.127, T.128, P.129, Y.132, P.134 Ligands: E9D.11, E9D.12 12 PLIP interactions: 7 interactions with chain N, 5 interactions with chain O Hydrophobic interactions: N:F.23, N:P.25, N:T.33, N:I.105, N:I.139, N:L.140, O:V.124, O:T.128, O:P.129, O:Y.132, O:P.134 Halogen bonds: N:D.29 E9D.8: 20 residues within 4Å: Chain O: F.23, P.25, L.30, T.33, W.102, I.105, S.106, F.110, Y.118, L.140 Chain T: V.124, W.125, T.128, P.129, Y.132, P.134, N.136, I.139 Chain V: N.136 Ligands: E9D.11 4 PLIP interactions: 3 interactions with chain O, 1 interactions with chain T Hydrophobic interactions: O:F.23, O:P.25, O:I.105, T:T.128 E9D.9: 20 residues within 4Å: Chain R: F.23, P.25, D.29, L.30, T.33, W.102, I.105, S.106, F.110, Y.118, I.139, L.140 Chain S: V.124, R.127, T.128, P.129, Y.132, P.134 Ligands: E9D.3, E9D.4 12 PLIP interactions: 7 interactions with chain R, 5 interactions with chain S Hydrophobic interactions: R:F.23, R:P.25, R:T.33, R:I.105, R:I.139, R:L.140, S:V.124, S:T.128, S:P.129, S:Y.132, S:P.134 Halogen bonds: R:D.29 E9D.10: 20 residues within 4Å: Chain D: V.124, W.125, T.128, P.129, Y.132, P.134, N.136, I.139 Chain F: N.136 Chain S: F.23, P.25, L.30, T.33, W.102, I.105, S.106, F.110, Y.118, L.140 Ligands: E9D.3 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain S Hydrophobic interactions: D:T.128, S:F.23, S:P.25, S:I.105 E9D.11: 20 residues within 4Å: Chain V: F.23, P.25, D.29, L.30, T.33, W.102, I.105, S.106, F.110, Y.118, I.139, L.140 Chain W: V.124, R.127, T.128, P.129, Y.132, P.134 Ligands: E9D.7, E9D.8 12 PLIP interactions: 7 interactions with chain V, 5 interactions with chain W Hydrophobic interactions: V:F.23, V:P.25, V:T.33, V:I.105, V:I.139, V:L.140, W:V.124, W:T.128, W:P.129, W:Y.132, W:P.134 Halogen bonds: V:D.29 E9D.12: 12 residues within 4Å: Chain N: N.136 Chain W: F.23, P.25, L.30, T.33, W.102, I.105, S.106, F.110, Y.118, L.140 Ligands: E9D.7 3 PLIP interactions: 3 interactions with chain W Hydrophobic interactions: W:F.23, W:P.25, W:I.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schlicksup, C.J. et al., Hepatitis B virus core protein allosteric modulators can distort and disrupt intact capsids. Elife (2018)

Release Date

2018-02-07

Peptides

Capsid protein: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

M
A

N
B

O
C

P
D

Q
A

R
B

S
C

T
D

U
A

V
B

W
C

X
D

Capsid protein

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