SMTL ID : 1nmb.1

THE STRUCTURE OF A COMPLEX BETWEEN THE NC10 ANTIBODY AND INFLUENZA VIRUS NEURAMINIDASE AND COMPARISON WITH THE OVERLAPPING BINDING SITE OF THE NC41 ANTIBODY

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 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-(1-2)-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

NAG-NAG-BMA-MAN-MAN-MAN-MAN.1: 21 residues within 4Å: Chain A: R.329, N.331, D.332, R.365, I.367, I.369, E.376, L.378, K.390, P.391, T.392, Q.393, G.394, F.454, L.455, G.456, Q.457 Chain C: R.104, D.106 Chain J: N.202, R.222 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.454 Hydrogen bonds: A:G.394 Water bridges: A:Q.393, A:G.394 NAG-NAG-BMA-MAN-MAN-MAN-MAN.5: 21 residues within 4Å: Chain D: R.329, N.331, D.332, R.365, I.367, I.369, E.376, L.378, K.390, P.391, T.392, Q.393, G.394, F.454, L.455, G.456, Q.457 Chain F: R.104, D.106 Chain G: N.202, R.222 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.454 Hydrogen bonds: D:G.394 Water bridges: D:Q.393, D:G.394 NAG-NAG-BMA-MAN-MAN-MAN-MAN.9: 21 residues within 4Å: Chain A: N.202, R.222 Chain G: R.329, N.331, D.332, R.365, I.367, I.369, E.376, L.378, K.390, P.391, T.392, Q.393, G.394, F.454, L.455, G.456, Q.457 Chain I: R.104, D.106 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:F.454 Hydrogen bonds: G:G.394 Water bridges: G:Q.393, G:G.394 NAG-NAG-BMA-MAN-MAN-MAN-MAN.13: 21 residues within 4Å: Chain D: N.202, R.222 Chain J: R.329, N.331, D.332, R.365, I.367, I.369, E.376, L.378, K.390, P.391, T.392, Q.393, G.394, F.454, L.455, G.456, Q.457 Chain L: R.104, D.106 4 PLIP interactions: 4 interactions with chain J Hydrophobic interactions: J:F.454 Hydrogen bonds: J:G.394 Water bridges: J:Q.393, J:G.394

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

NAG.2: 2 residues within 4Å: Chain A: N.147, W.439 No protein-ligand interaction detected (PLIP) NAG.3: 5 residues within 4Å: Chain A: E.84, F.85, N.87, Q.235, N.236 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.84 Hydrogen bonds: A:N.87, A:N.236 NAG.6: 2 residues within 4Å: Chain D: N.147, W.439 No protein-ligand interaction detected (PLIP) NAG.7: 5 residues within 4Å: Chain D: E.84, F.85, N.87, Q.235, N.236 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:E.84 Hydrogen bonds: D:N.87, D:N.236 NAG.10: 2 residues within 4Å: Chain G: N.147, W.439 No protein-ligand interaction detected (PLIP) NAG.11: 5 residues within 4Å: Chain G: E.84, F.85, N.87, Q.235, N.236 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:E.84 Hydrogen bonds: G:N.87, G:N.236 NAG.14: 2 residues within 4Å: Chain J: N.147, W.439 No protein-ligand interaction detected (PLIP) NAG.15: 5 residues within 4Å: Chain J: E.84, F.85, N.87, Q.235, N.236 3 PLIP interactions: 3 interactions with chain J Hydrophobic interactions: J:E.84 Hydrogen bonds: J:N.87, J:N.236

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: D.295, G.299, D.326, N.348 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.295, A:G.299, A:N.348, H2O.1 CA.8: 4 residues within 4Å: Chain D: D.295, G.299, D.326, N.348 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.295, D:G.299, D:N.348, H2O.4 CA.12: 4 residues within 4Å: Chain G: D.295, G.299, D.326, N.348 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.295, G:G.299, G:N.348, H2O.8 CA.16: 4 residues within 4Å: Chain J: D.295, G.299, D.326, N.348 4 PLIP interactions: 3 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:D.295, J:G.299, J:N.348, H2O.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malby, R.L. et al., The structure of a complex between the NC10 antibody and influenza virus neuraminidase and comparison with the overlapping binding site of the NC41 antibody. Structure (1994)

Release Date

1995-09-15

Peptides

N9 NEURAMINIDASE: ADGJ
FAB NC10: BEHK
FAB NC10: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
N

D
N

G
N

J
N

B
L

E
L

H
L

K
L

C
H

F
H

I
H

L
H

N9 NEURAMINIDASE

FAB NC10

FAB NC10

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