SMTL ID : 3jd7.2 (3 other biounits)

The novel asymmetric entry intermediate of a picornavirus captured with nanodiscs

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-5-5-5-5-mer

Ligands

5 x PLM: PALMITIC ACID(Non-covalent)

PLM.1: 10 residues within 4Å: Chain A: I.92, P.94, R.95, L.114, L.116, Y.143, P.165, M.178, N.211, M.213 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.92, A:I.92, A:P.94, A:L.114, A:L.116, A:Y.143, A:Y.143, A:Y.143 Hydrogen bonds: A:N.211 Salt bridges: A:R.95 PLM.2: 10 residues within 4Å: Chain E: I.92, P.94, R.95, L.114, L.116, Y.143, P.165, M.178, N.211, M.213 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:I.92, E:I.92, E:P.94, E:L.114, E:L.116, E:Y.143, E:Y.143, E:Y.143 Hydrogen bonds: E:N.211 Salt bridges: E:R.95 PLM.3: 10 residues within 4Å: Chain I: I.92, P.94, R.95, L.114, L.116, Y.143, P.165, M.178, N.211, M.213 10 PLIP interactions: 10 interactions with chain I Hydrophobic interactions: I:I.92, I:I.92, I:P.94, I:L.114, I:L.116, I:Y.143, I:Y.143, I:Y.143 Hydrogen bonds: I:N.211 Salt bridges: I:R.95 PLM.4: 10 residues within 4Å: Chain M: I.92, P.94, R.95, L.114, L.116, Y.143, P.165, M.178, N.211, M.213 10 PLIP interactions: 10 interactions with chain M Hydrophobic interactions: M:I.92, M:I.92, M:P.94, M:L.114, M:L.116, M:Y.143, M:Y.143, M:Y.143 Hydrogen bonds: M:N.211 Salt bridges: M:R.95 PLM.5: 10 residues within 4Å: Chain Q: I.92, P.94, R.95, L.114, L.116, Y.143, P.165, M.178, N.211, M.213 10 PLIP interactions: 10 interactions with chain Q Hydrophobic interactions: Q:I.92, Q:I.92, Q:P.94, Q:L.114, Q:L.116, Q:Y.143, Q:Y.143, Q:Y.143 Hydrogen bonds: Q:N.211 Salt bridges: Q:R.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, H. et al., The novel asymmetric entry intermediate of a picornavirus captured with nanodiscs. Sci Adv (2016)

Release Date

2016-09-14

Peptides

Capsid protein VP1: AEIMQ
Capsid protein VP2: BFJNR
Capsid protein VP3: CGKOS
Capsid protein VP4: DHLPT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

E
1

I
1

M
1

Q
1

B
2

F
2

J
2

N
2

R
2

C
3

G
3

K
3

O
3

S
3

D
4

H
4

L
4

P
4

T
4

Capsid protein VP1

Capsid protein VP2

Capsid protein VP3

Capsid protein VP4

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