SMTL ID : 5e64.1 (1 other biounit)

Hemagglutinin-esterase-fusion protein structure of influenza D virus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-3-3-mer

Ligands

6 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.1: 14 residues within 4Å: Chain A: N.128, T.130, Q.131, N.328, A.329, E.332, L.335, Q.336, K.344 Chain C: K.216, N.218 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.344, A:E.332, A:E.332 Water bridges: A:E.331, A:K.344, A:K.134, A:N.328 Hydrophobic interactions: A:T.130 NAG-NAG-BMA-MAN-MAN-MAN.2: 9 residues within 4Å: Chain A: N.328, E.331, E.332, L.335, K.344 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN.1 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.7: 14 residues within 4Å: Chain C: N.128, T.130, Q.131, N.328, A.329, E.332, L.335, Q.336, K.344 Chain E: K.216, N.218 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.8, NAG-NAG-BMA-MAN-MAN-MAN.8, NAG-NAG-BMA-MAN-MAN-MAN.8 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.344, C:E.332, C:E.332 Water bridges: C:E.331, C:K.344, C:K.134, C:N.328 Hydrophobic interactions: C:T.130 NAG-NAG-BMA-MAN-MAN-MAN.8: 9 residues within 4Å: Chain C: N.328, E.331, E.332, L.335, K.344 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.7, NAG-NAG-BMA-MAN-MAN-MAN.7, NAG-NAG-BMA-MAN-MAN-MAN.7, NAG-NAG-BMA-MAN-MAN-MAN.7 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.13: 14 residues within 4Å: Chain A: K.216, N.218 Chain E: N.128, T.130, Q.131, N.328, A.329, E.332, L.335, Q.336, K.344 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.14, NAG-NAG-BMA-MAN-MAN-MAN.14, NAG-NAG-BMA-MAN-MAN-MAN.14 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:K.344, E:E.332, E:E.332 Water bridges: E:K.344, E:K.134, E:N.328 Hydrophobic interactions: E:T.130 NAG-NAG-BMA-MAN-MAN-MAN.14: 9 residues within 4Å: Chain E: N.328, E.331, E.332, L.335, K.344 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.13, NAG-NAG-BMA-MAN-MAN-MAN.13, NAG-NAG-BMA-MAN-MAN-MAN.13, NAG-NAG-BMA-MAN-MAN-MAN.13 No protein-ligand interaction detected (PLIP)

6 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 9 residues within 4Å: Chain A: N.10, E.11, S.12, M.26 Chain B: G.19, G.20, V.21, A.22, G.23 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 13 residues within 4Å: Chain B: Q.55, L.56, D.59, N.107, N.111 Chain E: S.17, G.18, F.19, N.22, Q.422, G.424, T.425 Chain F: S.102 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain E Hydrogen bonds: B:D.59, E:S.17, E:N.22, E:Q.422 NAG-NAG.9: 9 residues within 4Å: Chain C: N.10, E.11, S.12, M.26 Chain D: G.19, G.20, V.21, A.22, G.23 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 13 residues within 4Å: Chain A: S.17, G.18, F.19, N.22, Q.422, G.424, T.425 Chain B: S.102 Chain D: Q.55, L.56, D.59, N.107, N.111 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:S.17, A:N.22, A:Q.422, D:D.59 NAG-NAG.15: 9 residues within 4Å: Chain E: N.10, E.11, S.12, M.26 Chain F: G.19, G.20, V.21, A.22, G.23 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 13 residues within 4Å: Chain C: S.17, G.18, F.19, N.22, Q.422, G.424, T.425 Chain D: S.102 Chain F: Q.55, L.56, D.59, N.107, N.111 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:S.17, C:N.22, C:Q.422, F:D.59

3 x CAC: CACODYLATE ION(Non-covalent)

CAC.5: 9 residues within 4Å: Chain A: D.54, S.55, R.56, S.82, G.83, V.114, N.115, W.320, H.357 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.55, A:G.83, A:N.115 CAC.11: 9 residues within 4Å: Chain C: D.54, S.55, R.56, S.82, G.83, V.114, N.115, W.320, H.357 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.55, C:G.83, C:N.115 CAC.17: 9 residues within 4Å: Chain E: D.54, S.55, R.56, S.82, G.83, V.114, N.115, W.320, H.357 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.55, E:G.83, E:N.115

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

NAG.6: 3 residues within 4Å: Chain B: N.58, N.61, E.65 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.58, B:N.61, B:E.65 NAG.12: 3 residues within 4Å: Chain D: N.58, N.61, E.65 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.58, D:N.61, D:E.65 NAG.18: 3 residues within 4Å: Chain F: N.58, N.61, E.65 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.58, F:N.61, F:E.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, H. et al., An Open Receptor-Binding Cavity of Hemagglutinin-Esterase-Fusion Glycoprotein from Newly-Identified Influenza D Virus: Basis for Its Broad Cell Tropism. PLoS Pathog. (2016)

Release Date

2016-03-23

Peptides

Hemagglutinin-esterase: ACE
Hemagglutinin-esterase: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Hemagglutinin-esterase

Hemagglutinin-esterase

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