SMTL ID : 5d7y.3 (3 other biounits)

Crystal structure of Hepatitis B virus T=4 capsid in complex with the allosteric modulator HAP18

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.89 Å

Oligo State

homo-24-mer

Ligands

12 x 58H: methyl (4R)-4-(2-chloro-4-fluorophenyl)-6-{[4-(3-hydroxypenta-1,4-diyn-3-yl)piperidin-1-yl]methyl}-2-(pyridin-2-yl)-1,4-dihydropyrimidine-5-carboxylate(Non-covalent)(Covalent)

58H.1: 17 residues within 4Å: Chain B: F.23, P.25, D.29, L.30, T.33, W.102, I.105, S.106, T.109, F.110, L.140 Chain C: V.124, W.125, T.128, Y.132, P.134, P.138 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:F.23, B:P.25, B:L.30, B:I.105, B:F.110, C:V.124, C:Y.132, C:P.134, C:P.138 Halogen bonds: B:D.29, C:T.128 58H.2: 13 residues within 4Å: Chain C: F.23, L.30, T.33, I.105, Y.118, L.140, S.141 Chain P: S.121, V.124, W.125, R.127, T.128, R.133 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain P Hydrophobic interactions: C:F.23, C:F.23, C:I.105, C:Y.118, P:V.124 Halogen bonds: C:T.33, P:T.128 Hydrogen bonds: P:R.133, P:R.133 58H.3: 17 residues within 4Å: Chain F: F.23, P.25, D.29, L.30, T.33, W.102, I.105, S.106, T.109, F.110, L.140 Chain G: V.124, W.125, T.128, Y.132, P.134, P.138 11 PLIP interactions: 5 interactions with chain G, 6 interactions with chain F Hydrophobic interactions: G:V.124, G:Y.132, G:P.134, G:P.138, F:F.23, F:P.25, F:L.30, F:I.105, F:F.110 Halogen bonds: G:T.128, F:D.29 58H.4: 7 residues within 4Å: Chain G: F.23, L.30, T.33, I.105, Y.118, L.140, S.141 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:F.23, G:F.23, G:I.105, G:Y.118 Halogen bonds: G:T.33 58H.5: 17 residues within 4Å: Chain J: F.23, P.25, D.29, L.30, T.33, W.102, I.105, S.106, T.109, F.110, L.140 Chain K: V.124, W.125, T.128, Y.132, P.134, P.138 12 PLIP interactions: 7 interactions with chain J, 5 interactions with chain K Hydrophobic interactions: J:F.23, J:P.25, J:L.30, J:I.105, J:F.110, K:V.124, K:Y.132, K:P.134, K:P.138 Hydrogen bonds: J:T.109 Halogen bonds: J:D.29, K:T.128 58H.6: 7 residues within 4Å: Chain K: F.23, L.30, T.33, I.105, Y.118, L.140, S.141 5 PLIP interactions: 5 interactions with chain K Hydrophobic interactions: K:F.23, K:F.23, K:I.105, K:Y.118 Halogen bonds: K:T.33 58H.7: 17 residues within 4Å: Chain N: F.23, P.25, D.29, L.30, T.33, W.102, I.105, S.106, T.109, F.110, L.140 Chain O: V.124, W.125, T.128, Y.132, P.134, P.138 11 PLIP interactions: 6 interactions with chain N, 5 interactions with chain O Hydrophobic interactions: N:F.23, N:P.25, N:L.30, N:I.105, N:F.110, O:V.124, O:Y.132, O:P.134, O:P.138 Halogen bonds: N:D.29, O:T.128 58H.8: 13 residues within 4Å: Chain O: F.23, L.30, T.33, I.105, Y.118, L.140, S.141 Chain T: S.121, V.124, W.125, R.127, T.128, R.133 9 PLIP interactions: 5 interactions with chain O, 4 interactions with chain T Hydrophobic interactions: O:F.23, O:F.23, O:I.105, O:Y.118, T:V.124 Halogen bonds: O:T.33, T:T.128 Hydrogen bonds: T:R.133, T:R.133 58H.9: 17 residues within 4Å: Chain R: F.23, P.25, D.29, L.30, T.33, W.102, I.105, S.106, T.109, F.110, L.140 Chain S: V.124, W.125, T.128, Y.132, P.134, P.138 11 PLIP interactions: 6 interactions with chain R, 5 interactions with chain S Hydrophobic interactions: R:F.23, R:P.25, R:L.30, R:I.105, R:F.110, S:V.124, S:Y.132, S:P.134, S:P.138 Halogen bonds: R:D.29, S:T.128 58H.10: 13 residues within 4Å: Chain D: S.121, V.124, W.125, R.127, T.128, R.133 Chain S: F.23, L.30, T.33, I.105, Y.118, L.140, S.141 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain S Hydrophobic interactions: D:V.124, S:F.23, S:F.23, S:I.105, S:Y.118 Hydrogen bonds: D:R.133, D:R.133 Halogen bonds: D:T.128, S:T.33 58H.11: 17 residues within 4Å: Chain V: F.23, P.25, D.29, L.30, T.33, W.102, I.105, S.106, T.109, F.110, L.140 Chain W: V.124, W.125, T.128, Y.132, P.134, P.138 11 PLIP interactions: 5 interactions with chain W, 6 interactions with chain V Hydrophobic interactions: W:V.124, W:Y.132, W:P.134, W:P.138, V:F.23, V:P.25, V:L.30, V:I.105, V:F.110 Halogen bonds: W:T.128, V:D.29 58H.12: 7 residues within 4Å: Chain W: F.23, L.30, T.33, I.105, Y.118, L.140, S.141 5 PLIP interactions: 5 interactions with chain W Hydrophobic interactions: W:F.23, W:F.23, W:I.105, W:Y.118 Halogen bonds: W:T.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Venkatakrishnan, B. et al., Hepatitis B Virus Capsids Have Diverse Structural Responses to Small-Molecule Ligands Bound to the Heteroaryldihydropyrimidine Pocket. J.Virol. (2016)

Release Date

2016-02-17

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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