SMTL ID : 2aeq.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 3.00 Å

Oligo State

hetero-4-4-4-mer

Ligands

28 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)

NAG.1: 2 residues within 4Å: Chain A: N.72, W.363 Ligand excluded by PLIP NAG.2: 6 residues within 4Å: Chain A: Y.10, N.12, S.14, K.15, E.339 Ligands: NAG.3 Ligand excluded by PLIP NAG.3: 1 residues within 4Å: Ligands: NAG.2 Ligand excluded by PLIP NAG.4: 6 residues within 4Å: Chain A: I.159, N.160, Y.210, P.211, K.234 Ligands: NAG.5 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Ligands: NAG.4 Ligand excluded by PLIP NAG.6: 9 residues within 4Å: Chain A: E.125, N.126 Chain B: F.91, N.92, R.93, Y.94 Chain G: Y.379, G.380 Ligands: NAG.7 Ligand excluded by PLIP NAG.7: 8 residues within 4Å: Chain B: R.93 Chain G: I.318, N.319, R.320, Y.379 Ligands: NAG.6, MAN.8, MAN.10 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain D: N.72, W.363 Ligand excluded by PLIP NAG.13: 6 residues within 4Å: Chain D: Y.10, N.12, S.14, K.15, E.339 Ligands: NAG.14 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Ligands: NAG.13 Ligand excluded by PLIP NAG.15: 6 residues within 4Å: Chain D: I.159, N.160, Y.210, P.211, K.234 Ligands: NAG.16 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Ligands: NAG.15 Ligand excluded by PLIP NAG.17: 9 residues within 4Å: Chain D: E.125, N.126 Chain E: F.91, N.92, R.93, Y.94 Chain J: Y.379, G.380 Ligands: NAG.18 Ligand excluded by PLIP NAG.18: 8 residues within 4Å: Chain E: R.93 Chain J: I.318, N.319, R.320, Y.379 Ligands: NAG.17, MAN.19, MAN.21 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain G: N.72, W.363 Ligand excluded by PLIP NAG.24: 6 residues within 4Å: Chain G: Y.10, N.12, S.14, K.15, E.339 Ligands: NAG.25 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Ligands: NAG.24 Ligand excluded by PLIP NAG.26: 6 residues within 4Å: Chain G: I.159, N.160, Y.210, P.211, K.234 Ligands: NAG.27 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Ligands: NAG.26 Ligand excluded by PLIP NAG.28: 9 residues within 4Å: Chain D: Y.379, G.380 Chain G: E.125, N.126 Chain H: F.91, N.92, R.93, Y.94 Ligands: NAG.29 Ligand excluded by PLIP NAG.29: 8 residues within 4Å: Chain D: I.318, N.319, R.320, Y.379 Chain H: R.93 Ligands: NAG.28, MAN.30, MAN.32 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain J: N.72, W.363 Ligand excluded by PLIP NAG.35: 6 residues within 4Å: Chain J: Y.10, N.12, S.14, K.15, E.339 Ligands: NAG.36 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Ligands: NAG.35 Ligand excluded by PLIP NAG.37: 6 residues within 4Å: Chain J: I.159, N.160, Y.210, P.211, K.234 Ligands: NAG.38 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Ligands: NAG.37 Ligand excluded by PLIP NAG.39: 9 residues within 4Å: Chain A: Y.379, G.380 Chain J: E.125, N.126 Chain K: F.91, N.92, R.93, Y.94 Ligands: NAG.40 Ligand excluded by PLIP NAG.40: 8 residues within 4Å: Chain A: I.318, N.319, R.320, Y.379 Chain K: R.93 Ligands: NAG.39, MAN.41, MAN.43 Ligand excluded by PLIP

16 x MAN: alpha-D-mannopyranose(Non-covalent)(Non-functional Binders)

MAN.8: 6 residues within 4Å: Chain G: Q.317, R.320 Ligands: NAG.7, MAN.9, MAN.10, MAN.11 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Q.317, G:R.320 MAN.9: 1 residues within 4Å: Ligands: MAN.8 No protein-ligand interaction detected (PLIP) MAN.10: 6 residues within 4Å: Chain G: D.256, Q.317, R.320 Ligands: NAG.7, MAN.8, MAN.11 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Q.317 MAN.11: 2 residues within 4Å: Ligands: MAN.8, MAN.10 No protein-ligand interaction detected (PLIP) MAN.19: 6 residues within 4Å: Chain J: Q.317, R.320 Ligands: NAG.18, MAN.20, MAN.21, MAN.22 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:Q.317, J:R.320 MAN.20: 1 residues within 4Å: Ligands: MAN.19 No protein-ligand interaction detected (PLIP) MAN.21: 6 residues within 4Å: Chain J: D.256, Q.317, R.320 Ligands: NAG.18, MAN.19, MAN.22 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:Q.317 MAN.22: 2 residues within 4Å: Ligands: MAN.19, MAN.21 No protein-ligand interaction detected (PLIP) MAN.30: 6 residues within 4Å: Chain D: Q.317, R.320 Ligands: NAG.29, MAN.31, MAN.32, MAN.33 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.317, D:R.320 MAN.31: 1 residues within 4Å: Ligands: MAN.30 No protein-ligand interaction detected (PLIP) MAN.32: 6 residues within 4Å: Chain D: D.256, Q.317, R.320 Ligands: NAG.29, MAN.30, MAN.33 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.317 MAN.33: 2 residues within 4Å: Ligands: MAN.30, MAN.32 No protein-ligand interaction detected (PLIP) MAN.41: 6 residues within 4Å: Chain A: Q.317, R.320 Ligands: NAG.40, MAN.42, MAN.43, MAN.44 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.317, A:R.320 MAN.42: 1 residues within 4Å: Ligands: MAN.41 No protein-ligand interaction detected (PLIP) MAN.43: 6 residues within 4Å: Chain A: D.256, Q.317, R.320 Ligands: NAG.40, MAN.41, MAN.44 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.317 MAN.44: 2 residues within 4Å: Ligands: MAN.41, MAN.43 No protein-ligand interaction detected (PLIP)

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 light chain: BEHK
FAB heavy chain: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

J
A

B
L

E
L

H
L

K
L

C
H

F
H

I
H

L
H

neuraminidase

FAB light chain

FAB heavy chain

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