SMTL ID : 6vmz.1

Crystal Structure of a H5N1 influenza virus hemagglutinin with CBS1117

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-3-3-mer

Ligands

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 5 residues within 4Å: Chain A: N.169, N.240, D.241, A.242 Chain B: S.221 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.242 Hydrogen bonds: A:N.169, A:N.240, A:N.240 NAG.2: 2 residues within 4Å: Chain A: N.27, R.314 No protein-ligand interaction detected (PLIP) NAG.3: 1 residues within 4Å: Chain A: N.158 No protein-ligand interaction detected (PLIP) NAG.5: 5 residues within 4Å: Chain B: N.169, T.171, N.240, A.242 Chain C: S.221 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.242 Hydrogen bonds: B:N.169, B:N.240 NAG.6: 3 residues within 4Å: Chain B: Q.19, K.26, N.27 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:K.26 NAG.7: 1 residues within 4Å: Chain B: N.158 No protein-ligand interaction detected (PLIP) NAG.9: 5 residues within 4Å: Chain A: S.221 Chain C: N.169, N.240, D.241, A.242 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.242 Hydrogen bonds: C:N.169, C:N.240, C:N.240 NAG.10: 2 residues within 4Å: Chain C: Q.19, N.27 No protein-ligand interaction detected (PLIP)

3 x R3P: 2,6-dichloro-N-[1-(propan-2-yl)piperidin-4-yl]benzamide(Non-covalent)

R3P.4: 7 residues within 4Å: Chain A: H.32, Q.34, T.319 Chain D: V.18, W.21, I.45, T.49 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:W.21, D:I.45 Hydrogen bonds: A:T.319 R3P.8: 9 residues within 4Å: Chain B: H.32, A.33, Q.34, T.319 Chain E: V.18, W.21, I.45, V.48, T.49 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: B:T.319, E:I.45 Hydrogen bonds: B:T.319 Halogen bonds: E:I.45 R3P.11: 8 residues within 4Å: Chain C: H.32, Q.34, T.319 Chain F: V.18, W.21, I.45, V.48, T.49 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain C Hydrophobic interactions: F:W.21, F:I.45 Halogen bonds: F:I.45 Hydrogen bonds: C:T.319

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Antanasijevic, A. et al., Structure of avian influenza hemagglutinin in complex with a small molecule entry inhibitor. Life Sci Alliance (2020)

Release Date

2020-07-01

Peptides

Hemagglutinin: ABC
Hemagglutinin: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
B

E
D

F
F

Hemagglutinin

Hemagglutinin

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