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

Cryo-EM Structure of Hepatitis B virus T=4 capsid in complex with the antiviral molecule DBT1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-24-mer

Ligands

24 x U0A: 11-oxo-N-[2-(4-sulfamoylphenyl)ethyl]-10,11-dihydrodibenzo[b,f][1,4]thiazepine-8-carboxamide(Non-covalent)(Covalent)

U0A.1: 8 residues within 4Å: Chain A: F.23, P.25, L.30, T.33, W.102, I.105, S.106, T.109 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.33, A:T.109 Hydrogen bonds: A:T.33 pi-Stacking: A:W.102 U0A.2: 13 residues within 4Å: Chain B: F.23, P.25, T.33, W.102, I.105, S.106, L.140 Chain C: S.121, V.124, R.127, T.128, Y.132, P.138 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:V.124, C:V.124, C:R.127, C:T.128, C:P.138, B:T.33, B:I.105, B:L.140, B:L.140 U0A.3: 14 residues within 4Å: Chain C: F.23, P.25, T.33, W.102, I.105, S.106, T.109, I.139 Chain P: S.121, V.124, R.127, T.128, P.134, P.138 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain P Hydrophobic interactions: C:T.33, C:I.105, C:T.109, C:I.139, P:V.124, P:P.134 Hydrogen bonds: C:T.33, P:T.128 U0A.4: 18 residues within 4Å: Chain D: F.23, P.25, L.30, T.33, W.102, S.106, I.139 Chain F: F.18, S.121, V.124, W.125, R.127, T.128, P.129, Y.132, R.133, P.134, P.138 13 PLIP interactions: 9 interactions with chain F, 4 interactions with chain D Hydrophobic interactions: F:F.18, F:V.124, F:W.125, F:R.127, F:R.127, F:T.128, F:R.133, F:P.134, D:F.23, D:T.33, D:I.139 Hydrogen bonds: F:T.128, D:T.33 U0A.5: 19 residues within 4Å: Chain A: S.121, F.122, V.124, W.125, T.128, Y.132, R.133, P.134, A.137, P.138, I.139 Chain E: F.23, P.25, L.30, T.33, W.102, I.105, S.106, T.109 10 PLIP interactions: 4 interactions with chain E, 6 interactions with chain A Hydrophobic interactions: E:T.33, E:T.109, A:V.124, A:V.124, A:W.125, A:R.133, A:P.134 Hydrogen bonds: E:T.33, A:T.128 pi-Stacking: E:W.102 U0A.6: 13 residues within 4Å: Chain F: F.23, P.25, T.33, W.102, I.105, S.106, L.140 Chain G: S.121, V.124, R.127, T.128, Y.132, P.138 9 PLIP interactions: 5 interactions with chain G, 4 interactions with chain F Hydrophobic interactions: G:V.124, G:V.124, G:R.127, G:T.128, G:P.138, F:T.33, F:I.105, F:L.140, F:L.140 U0A.7: 8 residues within 4Å: Chain G: F.23, P.25, T.33, W.102, I.105, S.106, T.109, I.139 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:T.33, G:I.105, G:T.109, G:I.139 U0A.8: 7 residues within 4Å: Chain H: F.23, P.25, L.30, T.33, W.102, S.106, I.139 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:F.23, H:T.33, H:I.139 Hydrogen bonds: H:T.33 U0A.9: 19 residues within 4Å: Chain I: F.23, P.25, L.30, T.33, W.102, I.105, S.106, T.109 Chain M: S.121, F.122, V.124, W.125, T.128, Y.132, R.133, P.134, A.137, P.138, I.139 10 PLIP interactions: 4 interactions with chain I, 6 interactions with chain M Hydrophobic interactions: I:T.33, I:T.109, M:V.124, M:V.124, M:W.125, M:R.133, M:P.134 Hydrogen bonds: I:T.33, M:T.128 pi-Stacking: I:W.102 U0A.10: 13 residues within 4Å: Chain J: F.23, P.25, T.33, W.102, I.105, S.106, L.140 Chain K: S.121, V.124, R.127, T.128, Y.132, P.138 9 PLIP interactions: 4 interactions with chain J, 5 interactions with chain K Hydrophobic interactions: J:T.33, J:I.105, J:L.140, J:L.140, K:V.124, K:V.124, K:R.127, K:T.128, K:P.138 U0A.11: 8 residues within 4Å: Chain K: F.23, P.25, T.33, W.102, I.105, S.106, T.109, I.139 5 PLIP interactions: 5 interactions with chain K Hydrophobic interactions: K:T.33, K:I.105, K:T.109, K:I.139 Hydrogen bonds: K:T.33 U0A.12: 7 residues within 4Å: Chain L: F.23, P.25, L.30, T.33, W.102, S.106, I.139 4 PLIP interactions: 4 interactions with chain L Hydrophobic interactions: L:F.23, L:T.33, L:I.139 Hydrogen bonds: L:T.33 U0A.13: 8 residues within 4Å: Chain M: F.23, P.25, L.30, T.33, W.102, I.105, S.106, T.109 4 PLIP interactions: 4 interactions with chain M Hydrophobic interactions: M:T.33, M:T.109 Hydrogen bonds: M:T.33 pi-Stacking: M:W.102 U0A.14: 13 residues within 4Å: Chain N: F.23, P.25, T.33, W.102, I.105, S.106, L.140 Chain O: S.121, V.124, R.127, T.128, Y.132, P.138 9 PLIP interactions: 5 interactions with chain O, 4 interactions with chain N Hydrophobic interactions: O:V.124, O:V.124, O:R.127, O:T.128, O:P.138, N:T.33, N:I.105, N:L.140, N:L.140 U0A.15: 14 residues within 4Å: Chain O: F.23, P.25, T.33, W.102, I.105, S.106, T.109, I.139 Chain T: S.121, V.124, R.127, T.128, P.134, P.138 8 PLIP interactions: 5 interactions with chain O, 3 interactions with chain T Hydrophobic interactions: O:T.33, O:I.105, O:T.109, O:I.139, T:V.124, T:P.134 Hydrogen bonds: O:T.33, T:T.128 U0A.16: 18 residues within 4Å: Chain J: F.18, S.121, V.124, W.125, R.127, T.128, P.129, Y.132, R.133, P.134, P.138 Chain P: F.23, P.25, L.30, T.33, W.102, S.106, I.139 13 PLIP interactions: 9 interactions with chain J, 4 interactions with chain P Hydrophobic interactions: J:F.18, J:V.124, J:W.125, J:R.127, J:R.127, J:T.128, J:R.133, J:P.134, P:F.23, P:T.33, P:I.139 Hydrogen bonds: J:T.128, P:T.33 U0A.17: 8 residues within 4Å: Chain Q: F.23, P.25, L.30, T.33, W.102, I.105, S.106, T.109 4 PLIP interactions: 4 interactions with chain Q Hydrophobic interactions: Q:T.33, Q:T.109 Hydrogen bonds: Q:T.33 pi-Stacking: Q:W.102 U0A.18: 13 residues within 4Å: Chain R: F.23, P.25, T.33, W.102, I.105, S.106, L.140 Chain S: S.121, V.124, R.127, T.128, Y.132, P.138 9 PLIP interactions: 5 interactions with chain S, 4 interactions with chain R Hydrophobic interactions: S:V.124, S:V.124, S:R.127, S:T.128, S:P.138, R:T.33, R:I.105, R:L.140, R:L.140 U0A.19: 14 residues within 4Å: Chain D: S.121, V.124, R.127, T.128, P.134, P.138 Chain S: F.23, P.25, T.33, W.102, I.105, S.106, T.109, I.139 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain S Hydrophobic interactions: D:V.124, D:P.134, S:T.33, S:I.105, S:T.109, S:I.139 Hydrogen bonds: D:T.128, S:T.33 U0A.20: 18 residues within 4Å: Chain T: F.23, P.25, L.30, T.33, W.102, S.106, I.139 Chain V: F.18, S.121, V.124, W.125, R.127, T.128, P.129, Y.132, R.133, P.134, P.138 12 PLIP interactions: 4 interactions with chain T, 8 interactions with chain V Hydrophobic interactions: T:F.23, T:T.33, T:I.139, V:F.18, V:V.124, V:W.125, V:R.127, V:R.127, V:T.128, V:R.133, V:P.134 Hydrogen bonds: T:T.33 U0A.21: 19 residues within 4Å: Chain Q: S.121, F.122, V.124, W.125, T.128, Y.132, R.133, P.134, A.137, P.138, I.139 Chain U: F.23, P.25, L.30, T.33, W.102, I.105, S.106, T.109 10 PLIP interactions: 4 interactions with chain U, 6 interactions with chain Q Hydrophobic interactions: U:T.33, U:T.109, Q:V.124, Q:V.124, Q:W.125, Q:R.133, Q:P.134 Hydrogen bonds: U:T.33, Q:T.128 pi-Stacking: U:W.102 U0A.22: 13 residues within 4Å: Chain V: F.23, P.25, T.33, W.102, I.105, S.106, L.140 Chain W: S.121, V.124, R.127, T.128, Y.132, P.138 9 PLIP interactions: 4 interactions with chain V, 5 interactions with chain W Hydrophobic interactions: V:T.33, V:I.105, V:L.140, V:L.140, W:V.124, W:V.124, W:R.127, W:T.128, W:P.138 U0A.23: 8 residues within 4Å: Chain W: F.23, P.25, T.33, W.102, I.105, S.106, T.109, I.139 4 PLIP interactions: 4 interactions with chain W Hydrophobic interactions: W:T.33, W:I.105, W:T.109, W:I.139 U0A.24: 7 residues within 4Å: Chain X: F.23, P.25, L.30, T.33, W.102, S.106, I.139 4 PLIP interactions: 4 interactions with chain X Hydrophobic interactions: X:F.23, X:T.33, X:I.139 Hydrogen bonds: X:T.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schlicksup, C.J. et al., Local Stabilization of Subunit-Subunit Contacts Causes Global Destabilization of Hepatitis B Virus Capsids. Acs Chem.Biol. (2020)

Release Date

2020-06-03

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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