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

Cryo-EM Structure of Hepatitis B virus T=3 capsid in complex with the fluorescent allosteric modulator HAP-TAMRA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-18-mer

Ligands

6 x E9D: Heteroaryldihydropyrimidine tetramethylrodamine(Non-covalent)

E9D.1: 23 residues within 4Å: Chain A: V.124, W.125, R.127, T.128, Y.132, P.134 Chain B: F.23, F.24, P.25, D.29, L.30, T.33, W.102, I.105, S.106, T.109, F.110, Y.118, N.136, I.139, L.140, S.141 Chain J: P.144 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.23, B:F.23, B:P.25, B:L.30, B:T.33, B:I.139, A:Y.132 Halogen bonds: B:D.29 E9D.2: 22 residues within 4Å: Chain D: V.124, W.125, R.127, T.128, Y.132, P.134 Chain E: F.23, F.24, P.25, D.29, L.30, T.33, W.102, I.105, S.106, T.109, F.110, Y.118, N.136, I.139, L.140, S.141 8 PLIP interactions: 1 interactions with chain D, 7 interactions with chain E Hydrophobic interactions: D:Y.132, E:F.23, E:F.23, E:P.25, E:L.30, E:T.33, E:I.139 Halogen bonds: E:D.29 E9D.3: 22 residues within 4Å: Chain G: V.124, W.125, R.127, T.128, Y.132, P.134 Chain H: F.23, F.24, P.25, D.29, L.30, T.33, W.102, I.105, S.106, T.109, F.110, Y.118, N.136, I.139, L.140, S.141 9 PLIP interactions: 8 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:F.23, H:F.23, H:P.25, H:L.30, H:T.33, H:I.139, G:Y.132 Hydrogen bonds: H:Y.118 Halogen bonds: H:D.29 E9D.4: 23 residues within 4Å: Chain J: V.124, W.125, R.127, T.128, Y.132, P.134 Chain K: F.23, F.24, P.25, D.29, L.30, T.33, W.102, I.105, S.106, T.109, F.110, Y.118, N.136, I.139, L.140, S.141 Chain M: P.144 9 PLIP interactions: 8 interactions with chain K, 1 interactions with chain J Hydrophobic interactions: K:F.23, K:F.23, K:P.25, K:L.30, K:T.33, K:I.139, J:Y.132 Hydrogen bonds: K:Y.118 Halogen bonds: K:D.29 E9D.5: 23 residues within 4Å: Chain A: P.144 Chain M: V.124, W.125, R.127, T.128, Y.132, P.134 Chain N: F.23, F.24, P.25, D.29, L.30, T.33, W.102, I.105, S.106, T.109, F.110, Y.118, N.136, I.139, L.140, S.141 9 PLIP interactions: 8 interactions with chain N, 1 interactions with chain M Hydrophobic interactions: N:F.23, N:F.23, N:P.25, N:L.30, N:T.33, N:I.139, M:Y.132 Hydrogen bonds: N:Y.118 Halogen bonds: N:D.29 E9D.6: 22 residues within 4Å: Chain P: V.124, W.125, R.127, T.128, Y.132, P.134 Chain Q: F.23, F.24, P.25, D.29, L.30, T.33, W.102, I.105, S.106, T.109, F.110, Y.118, N.136, I.139, L.140, S.141 9 PLIP interactions: 8 interactions with chain Q, 1 interactions with chain P Hydrophobic interactions: Q:F.23, Q:F.23, Q:P.25, Q:L.30, Q:T.33, Q:I.139, P:Y.132 Hydrogen bonds: Q:Y.118 Halogen bonds: Q:D.29

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: ABCDEFGHIJKLMNOPQR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

C
A

D
C

E
B

F
A

G
C

H
B

I
A

J
C

K
B

L
A

M
C

N
B

O
A

P
C

Q
B

R
A

Capsid protein

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