SMTL ID : 5d7y.2 (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-20-mer

Ligands

10 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)

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: 5 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:V.124, C:Y.132, C:P.134, C:P.138, B:F.23, B:P.25, B:L.30, B:I.105, B:F.110 Halogen bonds: C:T.128, B:D.29 58H.2: 7 residues within 4Å: Chain C: F.23, L.30, T.33, I.105, Y.118, L.140, S.141 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.23, C:F.23, C:I.105, C:Y.118 Halogen bonds: C:T.33 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 12 PLIP interactions: 5 interactions with chain O, 7 interactions with chain N Hydrophobic interactions: O:V.124, O:Y.132, O:P.134, O:P.138, N:F.23, N:P.25, N:L.30, N:I.105, N:F.110 Halogen bonds: O:T.128, N:D.29 Hydrogen bonds: N:T.109 58H.8: 7 residues within 4Å: Chain O: F.23, L.30, T.33, I.105, Y.118, L.140, S.141 5 PLIP interactions: 5 interactions with chain O Hydrophobic interactions: O:F.23, O:F.23, O:I.105, O:Y.118 Halogen bonds: O:T.33 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: 5 interactions with chain S, 6 interactions with chain R Hydrophobic interactions: S:V.124, S:Y.132, S:P.134, S:P.138, R:F.23, R:P.25, R:L.30, R:I.105, R:F.110 Halogen bonds: S:T.128, R:D.29 58H.10: 7 residues within 4Å: Chain S: F.23, L.30, T.33, I.105, Y.118, L.140, S.141 5 PLIP interactions: 5 interactions with chain S Hydrophobic interactions: S:F.23, S:F.23, S:I.105, S:Y.118 Halogen bonds: S: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: ABCDEFGHIJKLMNOPQRST

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

Capsid protein

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