SMTL ID : 3znl.1

H5 Haemagglutinin in Complex with 6-O-Sulfo-Sialyl-Lewis X (Sulfated Lewis X)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-3-3-mer

Ligands

3 x NGS- GLA- SIA- FUC: N-acetyl-alpha-neuraminic acid-(2-3)-alpha-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose(Post Translational Modification)

NGS-GLA-SIA-FUC.1: 15 residues within 4Å: Chain A: Y.91, L.129, G.130, V.131, S.132, S.133, W.149, H.179, N.182, E.186, K.189, L.190, K.218, Q.222, G.224 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.218, A:Q.222, A:Q.222, A:V.131, A:S.133, A:H.179, A:N.182, A:E.186, A:Q.222 Water bridges: A:S.223, A:G.224 Salt bridges: A:K.189 Hydrophobic interactions: A:W.149 NGS-GLA-SIA-FUC.2: 15 residues within 4Å: Chain C: Y.91, L.129, G.130, V.131, S.132, S.133, W.149, H.179, N.182, E.186, K.189, L.190, K.218, Q.222, G.224 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:K.218, C:K.218, C:Q.222, C:Q.222, C:V.131, C:S.133, C:H.179, C:N.182, C:E.186, C:Q.222 Salt bridges: C:K.189 Hydrophobic interactions: C:W.149 Water bridges: C:G.224 NGS-GLA-SIA-FUC.3: 14 residues within 4Å: Chain E: Y.91, L.129, V.131, S.132, S.133, W.149, H.179, N.182, E.186, K.189, L.190, K.218, Q.222, G.224 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:K.218, E:Q.222, E:Q.222, E:V.131, E:S.133, E:H.179, E:N.182, E:E.186, E:Q.222 Salt bridges: E:K.189 Hydrophobic interactions: E:W.149 Water bridges: E:G.224

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

NAG.4: 2 residues within 4Å: Chain A: K.22, N.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.23 Water bridges: A:N.23 NAG.5: 3 residues within 4Å: Chain A: N.165, N.236, A.238 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.165 NAG.6: 3 residues within 4Å: Chain B: E.147, E.150, N.154 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.156, B:T.156 NAG.8: 2 residues within 4Å: Chain C: K.22, N.23 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.23 Water bridges: C:K.22, C:N.23 NAG.9: 2 residues within 4Å: Chain C: N.165, N.236 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.165 NAG.10: 4 residues within 4Å: Chain D: E.147, E.150, N.154, T.156 No protein-ligand interaction detected (PLIP) NAG.12: 2 residues within 4Å: Chain E: K.22, N.23 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.23 Water bridges: E:Q.15, E:N.23 NAG.13: 2 residues within 4Å: Chain E: N.165, N.236 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.165 NAG.14: 3 residues within 4Å: Chain F: E.147, E.150, N.154 No protein-ligand interaction detected (PLIP)

3 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.7: 6 residues within 4Å: Chain A: C.4 Chain B: W.14, H.25, Y.34, N.135, C.137 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.135 Salt bridges: B:H.25 EPE.11: 6 residues within 4Å: Chain C: C.4 Chain D: W.14, H.25, Y.34, N.135, C.137 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.135 Salt bridges: D:H.25 EPE.15: 5 residues within 4Å: Chain F: W.14, H.25, Y.34, N.135, C.137 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.135 Salt bridges: F:H.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiong, X. et al., Recognition of Sulphated and Fucosylated Receptor Sialosides by A/Vietnam/1194/2004 (H5N1) Influenza Virus. Virus Res. (2013)

Release Date

2013-09-25

Peptides

HAEMAGGLUTININ: ACE
HAEMAGGLUTININ: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

HAEMAGGLUTININ

HAEMAGGLUTININ

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