SMTL ID : 3kic.2 (3 other biounits)

Crystal structure of adeno-associated virus serotype 3B

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-20-mer

Ligands

20 x D5M: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE(Non-covalent)

D5M.1: 8 residues within 4Å: Chain A: V.418, P.419, F.629, H.630, P.631, S.632, F.638, G.639 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.419 Hydrogen bonds: A:G.639, A:G.639 pi-Stacking: A:H.630 D5M.2: 8 residues within 4Å: Chain B: V.418, P.419, F.629, H.630, P.631, S.632, F.638, G.639 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.419 Hydrogen bonds: B:G.639, B:G.639 pi-Stacking: B:H.630 D5M.3: 8 residues within 4Å: Chain C: V.418, P.419, F.629, H.630, P.631, S.632, F.638, G.639 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:P.419 Hydrogen bonds: C:G.639, C:G.639 pi-Stacking: C:H.630 D5M.4: 8 residues within 4Å: Chain D: V.418, P.419, F.629, H.630, P.631, S.632, F.638, G.639 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:P.419 Hydrogen bonds: D:G.639, D:G.639 pi-Stacking: D:H.630 D5M.5: 8 residues within 4Å: Chain E: V.418, P.419, F.629, H.630, P.631, S.632, F.638, G.639 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:P.419 Hydrogen bonds: E:G.639, E:G.639 pi-Stacking: E:H.630 D5M.6: 8 residues within 4Å: Chain F: V.418, P.419, F.629, H.630, P.631, S.632, F.638, G.639 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:P.419 Hydrogen bonds: F:G.639, F:G.639 pi-Stacking: F:H.630 D5M.7: 8 residues within 4Å: Chain G: V.418, P.419, F.629, H.630, P.631, S.632, F.638, G.639 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:P.419 Hydrogen bonds: G:G.639, G:G.639 pi-Stacking: G:H.630 D5M.8: 8 residues within 4Å: Chain H: V.418, P.419, F.629, H.630, P.631, S.632, F.638, G.639 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:P.419 Hydrogen bonds: H:G.639, H:G.639 pi-Stacking: H:H.630 D5M.9: 8 residues within 4Å: Chain I: V.418, P.419, F.629, H.630, P.631, S.632, F.638, G.639 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:P.419 Hydrogen bonds: I:G.639, I:G.639 pi-Stacking: I:H.630 D5M.10: 8 residues within 4Å: Chain J: V.418, P.419, F.629, H.630, P.631, S.632, F.638, G.639 4 PLIP interactions: 4 interactions with chain J Hydrophobic interactions: J:P.419 Hydrogen bonds: J:G.639, J:G.639 pi-Stacking: J:H.630 D5M.11: 8 residues within 4Å: Chain K: V.418, P.419, F.629, H.630, P.631, S.632, F.638, G.639 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:P.419 Hydrogen bonds: K:G.639, K:G.639 pi-Stacking: K:H.630 D5M.12: 8 residues within 4Å: Chain L: V.418, P.419, F.629, H.630, P.631, S.632, F.638, G.639 4 PLIP interactions: 4 interactions with chain L Hydrophobic interactions: L:P.419 Hydrogen bonds: L:G.639, L:G.639 pi-Stacking: L:H.630 D5M.13: 8 residues within 4Å: Chain M: V.418, P.419, F.629, H.630, P.631, S.632, F.638, G.639 4 PLIP interactions: 4 interactions with chain M Hydrophobic interactions: M:P.419 Hydrogen bonds: M:G.639, M:G.639 pi-Stacking: M:H.630 D5M.14: 8 residues within 4Å: Chain N: V.418, P.419, F.629, H.630, P.631, S.632, F.638, G.639 4 PLIP interactions: 4 interactions with chain N Hydrophobic interactions: N:P.419 Hydrogen bonds: N:G.639, N:G.639 pi-Stacking: N:H.630 D5M.15: 8 residues within 4Å: Chain O: V.418, P.419, F.629, H.630, P.631, S.632, F.638, G.639 4 PLIP interactions: 4 interactions with chain O Hydrophobic interactions: O:P.419 Hydrogen bonds: O:G.639, O:G.639 pi-Stacking: O:H.630 D5M.16: 8 residues within 4Å: Chain P: V.418, P.419, F.629, H.630, P.631, S.632, F.638, G.639 4 PLIP interactions: 4 interactions with chain P Hydrophobic interactions: P:P.419 Hydrogen bonds: P:G.639, P:G.639 pi-Stacking: P:H.630 D5M.17: 8 residues within 4Å: Chain Q: V.418, P.419, F.629, H.630, P.631, S.632, F.638, G.639 4 PLIP interactions: 4 interactions with chain Q Hydrophobic interactions: Q:P.419 Hydrogen bonds: Q:G.639, Q:G.639 pi-Stacking: Q:H.630 D5M.18: 8 residues within 4Å: Chain R: V.418, P.419, F.629, H.630, P.631, S.632, F.638, G.639 4 PLIP interactions: 4 interactions with chain R Hydrophobic interactions: R:P.419 Hydrogen bonds: R:G.639, R:G.639 pi-Stacking: R:H.630 D5M.19: 8 residues within 4Å: Chain S: V.418, P.419, F.629, H.630, P.631, S.632, F.638, G.639 4 PLIP interactions: 4 interactions with chain S Hydrophobic interactions: S:P.419 Hydrogen bonds: S:G.639, S:G.639 pi-Stacking: S:H.630 D5M.20: 8 residues within 4Å: Chain T: V.418, P.419, F.629, H.630, P.631, S.632, F.638, G.639 4 PLIP interactions: 4 interactions with chain T Hydrophobic interactions: T:P.419 Hydrogen bonds: T:G.639, T:G.639 pi-Stacking: T:H.630

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lerch, T.F. et al., The structure of adeno-associated virus serotype 3B (AAV-3B): insights into receptor binding and immune evasion. Virology (2010)

Release Date

2010-04-28

Peptides

Capsid protein VP1: ABCDEFGHIJKLMNOPQRST

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

Capsid protein VP1

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