SMTL ID : 4cqz.1

Crystal Structure of H5 (VN1194) Gln196Arg Mutant Haemagglutinin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-3-3-mer

Ligands

3 x NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG-GAL-SIA.1: 13 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, L.190, Q.222, G.224 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.222, A:Q.222, A:V.131, A:S.133, A:H.179, A:Q.222, A:Q.222 Water bridges: A:N.182, A:G.224 Hydrophobic interactions: A:W.149 NAG-GAL-SIA.6: 13 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, L.190, Q.222, G.224 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Q.222, C:Q.222, C:V.131, C:S.133, C:H.179, C:Q.222, C:Q.222 Water bridges: C:N.182, C:G.224 Hydrophobic interactions: C:W.149 NAG-GAL-SIA.11: 13 residues within 4Å: Chain E: Y.91, L.129, G.130, V.131, S.132, S.133, W.149, H.179, N.182, E.186, L.190, Q.222, G.224 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:Q.222, E:Q.222, E:V.131, E:S.133, E:H.179, E:Q.222, E:Q.222 Water bridges: E:N.182, E:G.224 Hydrophobic interactions: E:W.149

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)

NAG-NAG.2: 3 residues within 4Å: Chain A: N.165, N.236, A.238 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.236 NAG-NAG.7: 3 residues within 4Å: Chain C: N.165, N.236, A.238 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.236 NAG-NAG.12: 3 residues within 4Å: Chain E: N.165, N.236, A.238 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.236

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)(Post Translational Modification)

NAG-NAG.3: 4 residues within 4Å: Chain B: E.147, E.150, N.154, T.156 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain D: E.147, E.150, N.154, T.156 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain F: E.147, E.150, N.154, T.156 No protein-ligand interaction detected (PLIP)

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

NAG.4: 2 residues within 4Å: Chain A: K.22, N.23 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.22 Hydrogen bonds: A:N.23 NAG.9: 2 residues within 4Å: Chain C: K.22, N.23 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.22 Hydrogen bonds: C:N.23 NAG.14: 2 residues within 4Å: Chain E: K.22, N.23 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:K.22 Hydrogen bonds: E:N.23

3 x MPO: 3[N-MORPHOLINO]PROPANE SULFONIC ACID(Non-covalent)(Post Translational Modification)

MPO.5: 5 residues within 4Å: Chain B: W.14, H.25, Y.34, N.135, C.137 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.14, B:W.14 Salt bridges: B:H.25 MPO.10: 5 residues within 4Å: Chain D: W.14, H.25, Y.34, N.135, C.137 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:W.14, D:W.14 Salt bridges: D:H.25 MPO.15: 5 residues within 4Å: Chain F: W.14, H.25, Y.34, N.135, C.137 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:W.14, F:W.14 Salt bridges: F:H.25

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Xiong, X. et al., Enhanced Human Receptor Binding by H5 Haemagglutinins. Virology (2014)

Release Date

2014-05-28

Peptides

Hemagglutinin HA1: ACE
Hemagglutinin HA2: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Hemagglutinin HA1

Hemagglutinin HA2

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