SMTL ID : 4k3x.1

Crystal structure of a subtype H18 hemagglutinin homologue from A/flat-faced bat/Peru/033/2010 (H18N11)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN- MAN- FUL- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA-MAN-MAN-FUL-FUC.1: 3 residues within 4Å: Chain A: H.165, N.238, N.240 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:H.165 NAG-NAG-BMA-MAN-MAN-FUL-FUC.2: 1 residues within 4Å: Chain A: N.15 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-FUL-FUC.5: 4 residues within 4Å: Chain B: H.165, Q.167, N.238, N.240 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:H.165

1 x NAG- FUL- NAG- FUL: beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUL-NAG-FUL.3: 7 residues within 4Å: Chain A: K.49, N.263 Chain B: K.310 Chain D: N.60, T.61, Q.62, F.63 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:F.63, D:N.60 Water bridges: D:Q.62, D:Q.62, D:N.60 Hydrophobic interactions: B:K.310

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

NAG-NAG.4: 3 residues within 4Å: Chain A: C.277, D.278, N.289 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain C: Q.167, N.240 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: C.277, D.278, N.289 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain E: N.145, T.147, E.161, Y.162 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.161 NAG-NAG.12: 4 residues within 4Å: Chain F: N.145, T.147, E.161, Y.162 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.161

1 x NAG- NAG- BMA- BMA- FUL: beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA-FUL.6: 5 residues within 4Å: Chain B: T.262, N.263 Chain E: N.60, Q.62, F.63 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:Q.62, E:F.63, E:N.60 Water bridges: F:D.86

1 x NAG- FUL- NAG- FUC: beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUL-NAG-FUC.8: 7 residues within 4Å: Chain C: K.49, T.262, N.263, D.304 Chain F: N.60, Q.62, F.63 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain C Hydrogen bonds: F:Q.62, F:F.63, C:K.49, C:K.49

1 x NAG- FUL- NAG: beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-FUL-NAG.10: 4 residues within 4Å: Chain D: N.145, D.151, E.161, Y.162 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.161

12 x P4G: 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE(Non-covalent)

P4G.13: 6 residues within 4Å: Chain A: D.100, I.204, N.209, W.232, G.233, V.234 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.204 Hydrogen bonds: A:N.209, A:V.234 Water bridges: A:Y.211 P4G.15: 4 residues within 4Å: Chain B: S.32, H.34 Chain E: W.21, T.49 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.32 Water bridges: B:T.318 P4G.16: 5 residues within 4Å: Chain B: N.209, W.232, G.233, V.234 Chain F: I.73 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain B Hydrophobic interactions: F:I.73 Hydrogen bonds: B:V.234 Water bridges: B:D.100 P4G.17: 5 residues within 4Å: Chain B: H.41, N.42, G.43, E.272, I.285 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:H.41 P4G.19: 1 residues within 4Å: Chain C: H.41 No protein-ligand interaction detected (PLIP) P4G.20: 3 residues within 4Å: Chain C: H.34 Chain F: W.21, T.49 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.32 Water bridges: C:T.318, C:T.318 P4G.21: 5 residues within 4Å: Chain A: S.32 Chain D: W.21, T.49, V.52 Ligands: P4G.22 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:V.52 Hydrogen bonds: A:S.32 Water bridges: A:T.318, A:T.318 P4G.22: 5 residues within 4Å: Chain A: H.12 Chain D: I.18, G.20, W.21 Ligands: P4G.21 No protein-ligand interaction detected (PLIP) P4G.23: 6 residues within 4Å: Chain D: N.116, N.117, Q.120 Chain E: N.116, Q.120 Chain F: N.116 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Q.120 Hydrogen bonds: D:N.116, D:Q.120 P4G.24: 5 residues within 4Å: Chain B: H.12 Chain E: I.18, G.20, W.21, T.41 No protein-ligand interaction detected (PLIP) P4G.25: 7 residues within 4Å: Chain C: H.12 Chain F: I.18, G.20, W.21, T.41, Q.42, V.45 No protein-ligand interaction detected (PLIP) P4G.26: 4 residues within 4Å: Chain D: D.109, A.113 Chain F: A.113, N.114 No protein-ligand interaction detected (PLIP)

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

NAG.14: 2 residues within 4Å: Chain B: D.278, N.289 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:N.289 Hydrogen bonds: B:D.278, B:N.289 Water bridges: B:D.278, B:D.278 NAG.18: 1 residues within 4Å: Chain C: N.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tong, S. et al., New world bats harbor diverse influenza a viruses. Plos Pathog. (2013)

Release Date

2013-10-23

Peptides

Hemagglutinin HA1: ABC
Hemagglutinin HA2: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
B

E
D

F
F

Hemagglutinin HA1

Hemagglutinin HA2