SMTL ID : 2aep.1

An epidemiologically significant epitope of a 1998 influenza virus neuraminidase forms a highly hydrated interface in the NA-antibody complex.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-4-4-4-mer

Ligands

4 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.1: 13 residues within 4Å: Chain A: N.126 Chain C: N.92, R.93, Y.94 Chain G: D.256, Q.317, I.318, N.319, R.320, Y.379, G.380, T.381 Ligands: MAN.10 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:N.319, G:R.320, G:N.319, G:N.319, G:R.320 Water bridges: G:N.319, G:R.320 NAG-NAG-BMA-MAN-MAN-MAN-MAN.11: 13 residues within 4Å: Chain D: N.126 Chain F: N.92, R.93, Y.94 Chain J: D.256, Q.317, I.318, N.319, R.320, Y.379, G.380, T.381 Ligands: MAN.20 5 PLIP interactions: 5 interactions with chain J Hydrogen bonds: J:N.319, J:R.320, J:N.319, J:N.319, J:R.320 Water bridges: J:N.319, J:R.320 NAG-NAG-BMA-MAN-MAN-MAN-MAN.21: 13 residues within 4Å: Chain D: D.256, Q.317, I.318, N.319, R.320, Y.379, G.380, T.381 Chain G: N.126 Chain I: N.92, R.93, Y.94 Ligands: MAN.30 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.319, D:R.320, D:N.319, D:N.319, D:R.320 Water bridges: D:N.319, D:R.320 NAG-NAG-BMA-MAN-MAN-MAN-MAN.31: 13 residues within 4Å: Chain A: D.256, Q.317, I.318, N.319, R.320, Y.379, G.380, T.381 Chain J: N.126 Chain L: N.92, R.93, Y.94 Ligands: MAN.40 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.319, A:R.320, A:N.319, A:N.319, A:R.320 Water bridges: A:N.319, A:R.320

8 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.2: 6 residues within 4Å: Chain A: I.159, N.160, T.162, V.233, K.234 Ligands: NAG.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.160, A:T.162 Water bridges: A:T.162 GLC.9: 11 residues within 4Å: Chain A: S.171, S.173 Chain B: R.100, D.102, N.106, D.108, Y.109 Chain C: Y.49, R.54, Y.55, S.56 11 PLIP interactions: 6 interactions with chain B, 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:R.100, B:D.102, B:D.102, B:N.106, B:D.108, B:Y.109, C:Y.49, C:S.56, C:S.56, A:S.171 Water bridges: A:S.173 GLC.12: 6 residues within 4Å: Chain D: I.159, N.160, T.162, V.233, K.234 Ligands: NAG.15 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.160, D:T.162 Water bridges: D:T.162 GLC.19: 11 residues within 4Å: Chain D: S.171, S.173 Chain E: R.100, D.102, N.106, D.108, Y.109 Chain F: Y.49, R.54, Y.55, S.56 11 PLIP interactions: 6 interactions with chain E, 2 interactions with chain D, 3 interactions with chain F Hydrogen bonds: E:R.100, E:D.102, E:D.102, E:N.106, E:D.108, E:Y.109, D:S.171, F:Y.49, F:S.56, F:S.56 Water bridges: D:S.173 GLC.22: 6 residues within 4Å: Chain G: I.159, N.160, T.162, V.233, K.234 Ligands: NAG.25 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:N.160, G:T.162 Water bridges: G:T.162 GLC.29: 11 residues within 4Å: Chain G: S.171, S.173 Chain H: R.100, D.102, N.106, D.108, Y.109 Chain I: Y.49, R.54, Y.55, S.56 11 PLIP interactions: 3 interactions with chain I, 2 interactions with chain G, 6 interactions with chain H Hydrogen bonds: I:Y.49, I:S.56, I:S.56, G:S.171, H:R.100, H:D.102, H:D.102, H:N.106, H:D.108, H:Y.109 Water bridges: G:S.173 GLC.32: 6 residues within 4Å: Chain J: I.159, N.160, T.162, V.233, K.234 Ligands: NAG.35 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:N.160, J:T.162 Water bridges: J:T.162 GLC.39: 11 residues within 4Å: Chain J: S.171, S.173 Chain K: R.100, D.102, N.106, D.108, Y.109 Chain L: Y.49, R.54, Y.55, S.56 11 PLIP interactions: 3 interactions with chain L, 2 interactions with chain J, 6 interactions with chain K Hydrogen bonds: L:Y.49, L:S.56, L:S.56, J:S.171, K:R.100, K:D.102, K:D.102, K:N.106, K:D.108, K:Y.109 Water bridges: J:S.173

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

NAG.3: 5 residues within 4Å: Chain A: E.9, N.12, S.14, Y.210 Ligands: NAG.5 Ligand excluded by PLIP NAG.4: 4 residues within 4Å: Chain A: R.69, N.72, W.363, I.395 Ligand excluded by PLIP NAG.5: 5 residues within 4Å: Chain A: N.160, Y.210, P.211 Ligands: GLC.2, NAG.3 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.255, S.258 Ligand excluded by PLIP NAG.13: 5 residues within 4Å: Chain D: E.9, N.12, S.14, Y.210 Ligands: NAG.15 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain D: R.69, N.72, W.363, I.395 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain D: N.160, Y.210, P.211 Ligands: GLC.12, NAG.13 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain D: N.255, S.258 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain G: E.9, N.12, S.14, Y.210 Ligands: NAG.25 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain G: R.69, N.72, W.363, I.395 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain G: N.160, Y.210, P.211 Ligands: GLC.22, NAG.23 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain G: N.255, S.258 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain J: E.9, N.12, S.14, Y.210 Ligands: NAG.35 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain J: R.69, N.72, W.363, I.395 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain J: N.160, Y.210, P.211 Ligands: GLC.32, NAG.33 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain J: N.255, S.258 Ligand excluded by PLIP

4 x CA: CALCIUM ION(Non-covalent)

CA.7: 6 residues within 4Å: Chain A: D.219, G.223, D.250, G.271, H.273, G.274 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.219, A:G.223, A:D.250, A:G.271, A:H.273, H2O.4 CA.17: 6 residues within 4Å: Chain D: D.219, G.223, D.250, G.271, H.273, G.274 6 PLIP interactions: 5 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.219, D:G.223, D:D.250, D:G.271, D:H.273, H2O.24 CA.27: 6 residues within 4Å: Chain G: D.219, G.223, D.250, G.271, H.273, G.274 6 PLIP interactions: 5 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.219, G:G.223, G:D.250, G:G.271, G:H.273, H2O.43 CA.37: 6 residues within 4Å: Chain J: D.219, G.223, D.250, G.271, H.273, G.274 6 PLIP interactions: 5 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:D.219, J:G.223, J:D.250, J:G.271, J:H.273, H2O.63

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

SO4.8: 5 residues within 4Å: Chain A: R.44, D.77, R.218, R.297, Y.332 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.332, A:Y.332 Water bridges: A:R.44 Salt bridges: A:R.44, A:R.218, A:R.297 SO4.18: 5 residues within 4Å: Chain D: R.44, D.77, R.218, R.297, Y.332 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Y.332, D:Y.332 Water bridges: D:R.44 Salt bridges: D:R.44, D:R.218, D:R.297 SO4.28: 5 residues within 4Å: Chain G: R.44, D.77, R.218, R.297, Y.332 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:Y.332, G:Y.332 Water bridges: G:R.44 Salt bridges: G:R.44, G:R.218, G:R.297 SO4.38: 5 residues within 4Å: Chain J: R.44, D.77, R.218, R.297, Y.332 6 PLIP interactions: 6 interactions with chain J Hydrogen bonds: J:Y.332, J:Y.332 Water bridges: J:R.44 Salt bridges: J:R.44, J:R.218, J:R.297

4 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.10: 4 residues within 4Å: Chain C: Q.27, R.93 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN.1 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.93, C:R.93 MAN.20: 4 residues within 4Å: Chain F: Q.27, R.93 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.11, NAG-NAG-BMA-MAN-MAN-MAN-MAN.11 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.93, F:R.93 MAN.30: 4 residues within 4Å: Chain I: Q.27, R.93 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.21, NAG-NAG-BMA-MAN-MAN-MAN-MAN.21 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:R.93, I:R.93 MAN.40: 4 residues within 4Å: Chain L: Q.27, R.93 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.31, NAG-NAG-BMA-MAN-MAN-MAN-MAN.31 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:R.93, L:R.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Venkatramani, L. et al., An Epidemiologically Significant Epitope of a 1998 Human Influenza Virus Neuraminidase Forms a Highly Hydrated Interface in the NA-Antibody Complex. J.Mol.Biol. (2006)

Release Date

2005-12-20

Peptides

neuraminidase: ADGJ
FAB heavy chain: BEHK
FAB light chain: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

J
A

B
H

E
H

H
H

K
H

C
L

F
L

I
L

L
L

neuraminidase

FAB heavy chain

FAB light chain

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