SMTL ID : 5u4w.1 (2 other biounits)

Cryo-EM Structure of Immature Zika Virus

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

12 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-functional Binders)(Non-covalent)

NAG.1: 6 residues within 4Å: Chain A: N.75, F.98, M.126 Chain B: C.45, E.46 Ligands: NAG.2 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:N.75, A:F.98 Hydrogen bonds: A:N.75, B:C.45 NAG.2: 2 residues within 4Å: Ligands: NAG.1, BMA.3 No protein-ligand interaction detected (PLIP) NAG.5: 5 residues within 4Å: Chain B: V.31, M.33, N.69, S.70 Ligands: NAG.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.31, B:M.33, B:N.69 NAG.6: 3 residues within 4Å: Chain B: G.30, V.31 Ligands: NAG.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.31 NAG.7: 6 residues within 4Å: Chain C: N.75, F.98, M.126 Chain D: C.45, E.46 Ligands: NAG.8 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:C.45, C:N.75 Hydrophobic interactions: C:N.75, C:F.98 NAG.8: 2 residues within 4Å: Ligands: NAG.7, BMA.9 No protein-ligand interaction detected (PLIP) NAG.11: 5 residues within 4Å: Chain D: V.31, M.33, N.69, S.70 Ligands: NAG.12 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.31, D:M.33, D:N.69 NAG.12: 3 residues within 4Å: Chain D: G.30, V.31 Ligands: NAG.11 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.31 NAG.13: 6 residues within 4Å: Chain E: N.75, F.98, M.126 Chain F: C.45, E.46 Ligands: NAG.14 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:N.75, E:F.98 Hydrogen bonds: E:N.75, F:C.45 NAG.14: 2 residues within 4Å: Ligands: NAG.13, BMA.15 No protein-ligand interaction detected (PLIP) NAG.17: 5 residues within 4Å: Chain F: V.31, M.33, N.69, S.70 Ligands: NAG.18 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:V.31, F:M.33, F:N.69 NAG.18: 3 residues within 4Å: Chain F: G.30, V.31 Ligands: NAG.17 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:V.31

6 x BMA: beta-D-mannopyranose(Non-covalent)

BMA.3: 3 residues within 4Å: Chain B: H.2 Ligands: NAG.2, BMA.4 No protein-ligand interaction detected (PLIP) BMA.4: 4 residues within 4Å: Chain B: H.2, L.3, T.4 Ligands: BMA.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.4 BMA.9: 3 residues within 4Å: Chain D: H.2 Ligands: NAG.8, BMA.10 No protein-ligand interaction detected (PLIP) BMA.10: 4 residues within 4Å: Chain D: H.2, L.3, T.4 Ligands: BMA.9 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.4 BMA.15: 3 residues within 4Å: Chain F: H.2 Ligands: NAG.14, BMA.16 No protein-ligand interaction detected (PLIP) BMA.16: 4 residues within 4Å: Chain F: H.2, L.3, T.4 Ligands: BMA.15 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:T.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prasad, V.M. et al., Structure of the immature Zika virus at 9 angstrom resolution. Nat. Struct. Mol. Biol. (2017)

Release Date

2017-01-11

Peptides

E protein: ACE
pr domain: BDF
Protein E: GIK
M protein: HJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
G

I
I

K
K

H
H

J
J

L
L

E protein

pr domain

Protein E

M protein

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