SMTL ID : 3m5j.1

Crystal structure of a H7 influenza virus hemagglutinin complexed with LSTb

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-3-3-mer

Ligands

1 x GAL- NAG- GAL- SIA: beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose

GAL-NAG-GAL-SIA.1: 11 residues within 4Å: Chain A: Y.92, G.128, A.129, T.130, S.131, W.146, L.148, H.178, E.185, L.189, R.215 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.148, A:L.189 Hydrogen bonds: A:A.129, A:A.129, A:S.131, A:H.178, A:R.215

2 x NAG- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-SIA.2: 11 residues within 4Å: Chain C: Y.92, G.128, A.129, T.130, S.131, W.146, L.148, H.178, E.185, L.189, R.215 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.189 Hydrogen bonds: C:A.129, C:A.129, C:S.131, C:H.178, C:E.181, C:R.215 NAG-SIA.3: 11 residues within 4Å: Chain E: Y.92, G.128, A.129, T.130, S.131, W.146, L.148, H.178, E.185, L.189, R.215 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:L.189 Hydrogen bonds: E:A.129, E:A.129, E:S.131, E:H.178, E:R.215

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

NAG.4: 3 residues within 4Å: Chain A: N.32, A.33, T.34 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.34, A:T.34 NAG.5: 7 residues within 4Å: Chain A: R.287 Chain B: E.72, Q.75, G.78, N.79, N.82 Chain E: R.108 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain E Hydrogen bonds: A:R.287, A:R.287, B:E.72, E:R.108 NAG.9: 3 residues within 4Å: Chain C: N.32, A.33, T.34 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.32 NAG.10: 6 residues within 4Å: Chain A: R.108 Chain D: E.72, Q.75, G.78, N.79, N.82 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.72 NAG.12: 3 residues within 4Å: Chain E: N.32, A.33, T.34 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.34 NAG.13: 6 residues within 4Å: Chain C: R.108 Chain F: E.72, Q.75, G.78, N.79, N.82 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:E.72, C:R.108

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 1 residues within 4Å: Chain B: H.106 No protein-ligand interaction detected (PLIP) GOL.7: 6 residues within 4Å: Chain B: R.54, L.55 Chain D: Y.94, E.97, L.98, A.101 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.54 GOL.8: 6 residues within 4Å: Chain B: R.170, I.171 Chain D: L.167, R.170 Chain F: E.128, R.170 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:R.170, D:R.170 GOL.11: 6 residues within 4Å: Chain D: R.54, L.55, K.58 Chain F: Y.94, E.97, L.98 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain D Hydrogen bonds: F:Y.94, F:E.97, D:R.54, D:K.58 Water bridges: F:E.97 GOL.14: 6 residues within 4Å: Chain B: Y.94, E.97 Chain F: R.54, L.55, K.58, L.99 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain F Hydrogen bonds: B:Y.94, B:Y.94, F:R.54, F:K.58 Water bridges: B:E.97, B:E.97, B:A.101, F:R.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, H. et al., Structures of receptor complexes of a North American H7N2 influenza hemagglutinin with a loop deletion in the receptor binding site. Plos Pathog. (2010)

Release Date

2010-09-22

Peptides

Hemagglutinin: ACE
Hemagglutinin: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Hemagglutinin

Hemagglutinin

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