SMTL ID : 4g93.3 (3 other biounits)

CRYSTAL STRUCTURE OF THE HUMAN HEPATITIS B VIRUS T = 4 CAPSID, ADYW STRAIN, in COMPLEX WITH THE PHENYLPROPENAMIDE ASSEMBLY ACCELERATOR AT-130

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.20 Å

Oligo State

homo-24-mer

Ligands

12 x 0YP: N-[(1E)-1-bromo-1-(2-methoxyphenyl)-3-oxo-3-(piperidin-1-yl)prop-1-en-2-yl]-4-nitrobenzamide(Non-covalent)

0YP.1: 15 residues within 4Å: Chain B: P.25, D.29, L.30, T.33, W.102, S.106, F.110, V.115, Y.118 Chain C: V.124, R.127, T.128, Y.132, R.133, P.134 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:P.25, B:V.115, C:R.127, C:T.128 Hydrogen bonds: B:S.106 0YP.2: 11 residues within 4Å: Chain C: P.25, D.29, L.30, T.33, W.102, S.106, Y.118 Chain P: R.127, T.128, Y.132, P.134 4 PLIP interactions: 3 interactions with chain P, 1 interactions with chain C Hydrophobic interactions: P:P.134, C:P.25 Hydrogen bonds: P:T.128, P:T.128 0YP.3: 15 residues within 4Å: Chain F: P.25, D.29, L.30, T.33, W.102, S.106, F.110, V.115, Y.118 Chain G: V.124, R.127, T.128, Y.132, R.133, P.134 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain G Hydrophobic interactions: F:P.25, F:V.115, G:R.127, G:T.128 Hydrogen bonds: F:S.106 0YP.4: 7 residues within 4Å: Chain G: P.25, D.29, L.30, T.33, W.102, S.106, Y.118 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:P.25 0YP.5: 15 residues within 4Å: Chain J: P.25, D.29, L.30, T.33, W.102, S.106, F.110, V.115, Y.118 Chain K: V.124, R.127, T.128, Y.132, R.133, P.134 5 PLIP interactions: 3 interactions with chain J, 2 interactions with chain K Hydrophobic interactions: J:P.25, J:V.115, K:R.127, K:T.128 Hydrogen bonds: J:S.106 0YP.6: 7 residues within 4Å: Chain K: P.25, D.29, L.30, T.33, W.102, S.106, Y.118 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:P.25 0YP.7: 15 residues within 4Å: Chain N: P.25, D.29, L.30, T.33, W.102, S.106, F.110, V.115, Y.118 Chain O: V.124, R.127, T.128, Y.132, R.133, P.134 5 PLIP interactions: 3 interactions with chain N, 2 interactions with chain O Hydrophobic interactions: N:P.25, N:V.115, O:R.127, O:T.128 Hydrogen bonds: N:S.106 0YP.8: 11 residues within 4Å: Chain O: P.25, D.29, L.30, T.33, W.102, S.106, Y.118 Chain T: R.127, T.128, Y.132, P.134 4 PLIP interactions: 3 interactions with chain T, 1 interactions with chain O Hydrophobic interactions: T:P.134, O:P.25 Hydrogen bonds: T:T.128, T:T.128 0YP.9: 15 residues within 4Å: Chain R: P.25, D.29, L.30, T.33, W.102, S.106, F.110, V.115, Y.118 Chain S: V.124, R.127, T.128, Y.132, R.133, P.134 5 PLIP interactions: 3 interactions with chain R, 2 interactions with chain S Hydrophobic interactions: R:P.25, R:V.115, S:R.127, S:T.128 Hydrogen bonds: R:S.106 0YP.10: 11 residues within 4Å: Chain D: R.127, T.128, Y.132, P.134 Chain S: P.25, D.29, L.30, T.33, W.102, S.106, Y.118 4 PLIP interactions: 1 interactions with chain S, 3 interactions with chain D Hydrophobic interactions: S:P.25, D:P.134 Hydrogen bonds: D:T.128, D:T.128 0YP.11: 15 residues within 4Å: Chain V: P.25, D.29, L.30, T.33, W.102, S.106, F.110, V.115, Y.118 Chain W: V.124, R.127, T.128, Y.132, R.133, P.134 5 PLIP interactions: 3 interactions with chain V, 2 interactions with chain W Hydrophobic interactions: V:P.25, V:V.115, W:R.127, W:T.128 Hydrogen bonds: V:S.106 0YP.12: 7 residues within 4Å: Chain W: P.25, D.29, L.30, T.33, W.102, S.106, Y.118 1 PLIP interactions: 1 interactions with chain W Hydrophobic interactions: W:P.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Katen, S.P. et al., Assembly-directed antivirals differentially bind quasiequivalent pockets to modify hepatitis B virus capsid tertiary and quaternary structure. Structure (2013)

Release Date

2013-07-24

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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