SMTL ID : 4uo0.1

Structure of the A_Equine_Richmond_07 H3 haemagglutinin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-3-3-mer

Ligands

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

NAG-NAG.1: 3 residues within 4Å: Chain A: N.53, I.274, I.276 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.276 NAG-NAG.2: 3 residues within 4Å: Chain A: R.62, N.63, F.94 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.285, N.298 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.22 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: S.45, N.285, V.297 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain E: N.53, I.274, D.275, I.276 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain E: R.62, N.63, F.94 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain E: P.284, N.285, V.297, N.298 Chain F: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain E: N.38, A.39, T.40 No protein-ligand interaction detected (PLIP)

4 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[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(Non-functional Binders)(Post Translational Modification)

NAG-NAG-BMA-MAN-MAN.3: 6 residues within 4Å: Chain A: N.165, I.242, M.244 Chain E: S.219, P.221, W.222 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:W.222 Hydrophobic interactions: A:I.242 NAG-NAG-BMA-MAN-MAN.10: 2 residues within 4Å: Chain C: N.63, F.94 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.11: 6 residues within 4Å: Chain A: S.219, R.220, P.221, W.222 Chain C: N.165, M.244 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.222 NAG-NAG-BMA-MAN-MAN.18: 6 residues within 4Å: Chain C: S.219, P.221, W.222 Chain E: N.165, I.242, M.244 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:I.242 Hydrogen bonds: C:W.222

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

NAG-NAG-BMA-FUC.5: 4 residues within 4Å: Chain A: N.8 Chain B: S.29, K.143 Ligands: BMA.23 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.143 Hydrogen bonds: B:S.29, B:K.143

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

NAG-NAG-BMA.7: 3 residues within 4Å: Chain A: N.38, A.39, T.40 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 5 residues within 4Å: Chain C: N.53, N.54, I.274, D.275, I.276 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 3 residues within 4Å: Chain C: N.38, T.40, T.318 No protein-ligand interaction detected (PLIP)

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

NAG-FUC.8: 6 residues within 4Å: Chain B: A.147, G.150, S.151, R.153, N.154, T.156 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.154, B:T.156, B:R.153 Hydrophobic interactions: B:N.154

1 x NAG- NAG- BMA- MAN- MAN- 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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG-NAG-BMA-MAN-MAN-FUC.13: 4 residues within 4Å: Chain C: N.22, G.23, T.24, E.35 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG-NAG-FUC.15: 6 residues within 4Å: Chain D: A.147, G.150, S.151, R.153, N.154, T.156 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.153 NAG-NAG-FUC.20: 1 residues within 4Å: Chain E: N.8 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.22: 5 residues within 4Å: Chain F: A.147, G.150, R.153, N.154, T.156 No protein-ligand interaction detected (PLIP)

1 x BMA: beta-D-mannopyranose(Non-functional Binders)

BMA.23: 1 residues within 4Å: Ligands: NAG-NAG-BMA-FUC.5 No protein-ligand interaction detected (PLIP)

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.24: 5 residues within 4Å: Chain A: G.124, F.125, T.126, V.166, T.167 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.126, A:T.126, A:T.167 Water bridges: A:N.165 EDO.25: 3 residues within 4Å: Chain A: R.208, K.238 Chain F: E.72 No protein-ligand interaction detected (PLIP) EDO.26: 7 residues within 4Å: Chain B: N.53, R.54, V.55, I.56, E.57 Chain E: K.27 Chain F: E.97 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:N.53, B:E.57 Water bridges: B:R.58, F:E.97 EDO.27: 5 residues within 4Å: Chain B: N.49, E.50, N.53, R.54 Chain E: D.32 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain B Water bridges: E:D.32, E:D.32 Hydrogen bonds: B:E.50, B:R.54 EDO.29: 2 residues within 4Å: Chain C: D.175, K.238 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.238, C:K.238 EDO.30: 4 residues within 4Å: Chain B: R.76 Chain C: D.104, A.106, S.107 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:D.104, C:S.107, C:S.107, B:R.76 Water bridges: C:A.106 EDO.31: 6 residues within 4Å: Chain C: L.316, T.318 Chain D: I.48, N.49, E.50, K.51 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.49, D:E.50, D:K.51 Water bridges: D:L.52 EDO.33: 4 residues within 4Å: Chain E: S.95, P.99, Y.100, R.224 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Y.100, E:Y.100, E:R.224, E:R.224 Water bridges: E:S.95 EDO.34: 6 residues within 4Å: Chain E: N.133, G.134, R.135, R.141, S.146, F.147 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:N.133, E:F.147 Water bridges: E:R.255, E:R.255 EDO.35: 7 residues within 4Å: Chain C: K.27 Chain D: E.97 Chain F: N.53, R.54, V.55, I.56, E.57 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:E.97, F:I.56 EDO.36: 5 residues within 4Å: Chain B: E.128 Chain F: R.127, E.128, A.130, R.170 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain F Hydrogen bonds: B:E.128, F:E.128, F:R.170 Water bridges: B:E.128, F:R.170, F:R.170 EDO.37: 4 residues within 4Å: Chain D: M.133 Chain F: R.127, H.159, Y.160 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:R.127, F:R.127, D:K.139 Water bridges: F:R.163

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

NAG.28: 2 residues within 4Å: Chain C: N.8 Chain D: S.29 No protein-ligand interaction detected (PLIP) NAG.32: 2 residues within 4Å: Chain E: A.21, N.22 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:A.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Collins, P.J. et al., Recent Evolution of Equine Influenza and the Origin of Canine Influenza. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-07-23

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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