SMTL ID : 2b8h.1

A/NWS/whale/Maine/1/84 (H1N9) reassortant influenza virus neuraminidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 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.65, W.357 Chain D: Y.386 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain B: N.65, W.357 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain C: N.65, W.357 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain C: Y.386 Chain D: N.65, W.357 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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(Post Translational Modification)

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.2: 19 residues within 4Å: Chain A: N.119, N.120 Chain D: R.247, N.249, D.250, R.283, I.285, V.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, F.372, L.373, G.374, Q.375 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.372 Hydrogen bonds: D:G.312, D:Q.375 Water bridges: D:Q.311, D:G.312, D:E.294, D:G.312, D:Q.313 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.6: 19 residues within 4Å: Chain B: R.247, N.249, D.250, R.283, I.285, V.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, F.372, L.373, G.374, Q.375 Chain C: N.119, N.120 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.372 Hydrogen bonds: B:G.312, B:Q.375 Water bridges: B:Q.311, B:G.312, B:G.312 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.8: 20 residues within 4Å: Chain C: R.247, N.249, D.250, R.283, I.285, V.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, F.372, L.373, G.374, Q.375 Chain D: N.119, N.120 Ligands: SO4.38 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.372 Hydrogen bonds: C:G.312 Water bridges: C:Q.311, C:G.312, C:G.312

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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(Post Translational Modification)

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.4: 19 residues within 4Å: Chain A: R.247, N.249, D.250, R.283, I.285, V.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, F.372, L.373, G.374, Q.375 Chain B: N.119, N.120 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.372 Hydrogen bonds: A:G.312, A:Q.375 Water bridges: A:Q.311, A:Q.311, A:E.294, A:G.312, A:Q.313

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

NAG.9: 6 residues within 4Å: Chain A: E.2, F.3, N.5, Q.153, N.154, V.228 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.2 Hydrogen bonds: A:N.5, A:Q.153, A:N.154 NAG.22: 6 residues within 4Å: Chain B: E.2, F.3, N.5, Q.153, N.154, V.228 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.2, B:N.5, B:N.5, B:Q.153 NAG.30: 5 residues within 4Å: Chain C: E.2, F.3, N.5, N.154, V.228 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.5, C:N.154, C:N.154 Water bridges: C:Q.153, C:Q.153 NAG.41: 5 residues within 4Å: Chain D: E.2, F.3, N.5, Q.153, N.154 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:F.3, D:N.5

29 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 4 residues within 4Å: Chain A: K.255, C.256, N.257, D.258 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain A: R.37, D.70, R.212, R.290, Y.324 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain A: N.128, R.130 Chain D: P.45, D.46 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain A: P.251, T.252, V.253 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain A: P.248, N.249 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain A: R.71, N.118 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain A: H.69, D.70 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain A: W.376, N.377 Chain B: P.117 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain B: K.255, C.256, N.257, D.258 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain B: R.37, D.70, R.290, Y.324 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain A: P.45, D.46 Chain B: N.128, R.130 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain B: R.71, N.118 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain B: I.68, H.69, D.70 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain B: W.376, N.377 Chain C: P.117 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain C: K.255, C.256, N.257, D.258 Ligand excluded by PLIP SO4.32: 5 residues within 4Å: Chain C: R.37, D.70, R.212, R.290, Y.324 Ligand excluded by PLIP SO4.33: 4 residues within 4Å: Chain B: P.45, D.46 Chain C: N.128, R.130 Ligand excluded by PLIP SO4.34: 4 residues within 4Å: Chain C: P.251, T.252, V.253, Y.260 Ligand excluded by PLIP SO4.35: 2 residues within 4Å: Chain C: P.248, N.249 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain C: R.71, N.118 Ligands: SO4.37 Ligand excluded by PLIP SO4.37: 4 residues within 4Å: Chain C: H.69, D.70, R.71 Ligands: SO4.36 Ligand excluded by PLIP SO4.38: 4 residues within 4Å: Chain C: I.285, S.286, V.287 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.8 Ligand excluded by PLIP SO4.40: 2 residues within 4Å: Chain C: W.376 Chain D: P.117 Ligand excluded by PLIP SO4.42: 2 residues within 4Å: Chain A: P.117 Chain D: W.376 Ligand excluded by PLIP SO4.43: 4 residues within 4Å: Chain D: K.255, C.256, N.257, D.258 Ligand excluded by PLIP SO4.44: 5 residues within 4Å: Chain D: R.37, D.70, R.212, R.290, Y.324 Ligand excluded by PLIP SO4.45: 5 residues within 4Å: Chain C: P.45, D.46 Chain D: N.128, R.129, R.130 Ligand excluded by PLIP SO4.46: 2 residues within 4Å: Chain D: R.71, N.118 Ligand excluded by PLIP SO4.47: 3 residues within 4Å: Chain D: I.68, H.69, D.70 Ligand excluded by PLIP

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.17: 4 residues within 4Å: Chain A: R.348, A.382, K.383, I.384 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain B: R.348, K.383, I.384 Ligand excluded by PLIP CL.39: 4 residues within 4Å: Chain C: R.348, A.382, K.383, I.384 Ligand excluded by PLIP CL.48: 3 residues within 4Å: Chain D: R.348, K.383, I.384 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.19: 1 residues within 4Å: Chain A: W.185 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.173, A:Y.175, A:W.185 GOL.20: 6 residues within 4Å: Chain A: R.26 Chain B: H.63, N.65, G.66, T.67, Y.74 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.26, A:R.26, B:Q.55 Water bridges: B:S.72, B:S.72 GOL.21: 4 residues within 4Å: Chain A: N.141, S.165, A.166, T.167 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.141, A:A.166, A:T.167 Water bridges: A:N.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smith, B.J. et al., Structure of a calcium-deficient form of influenza virus neuraminidase: implications for substrate binding. Acta Crystallogr.,Sect.D (2006)

Release Date

2006-09-05

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Neuraminidase