SMTL ID : 1nma.1

N9 NEURAMINIDASE COMPLEXES WITH ANTIBODIES NC41 AND NC10: EMPIRICAL FREE-ENERGY CALCULATIONS CAPTURE SPECIFICITY TRENDS OBSERVED WITH MUTANT BINDING DATA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-4-4-4-mer

Ligands

4 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-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.1: 21 residues within 4Å: Chain A: R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, R.308, P.309, T.310, Q.311, G.312, L.373, G.374, Q.375 Chain C: Y.103, R.104, D.106 Chain D: N.120, R.140 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:T.310, A:R.247, A:D.250, A:R.283, A:I.285, C:R.104, C:D.106, A:G.312, A:G.312 NAG-NAG-BMA-MAN-MAN-MAN.3: 21 residues within 4Å: Chain D: R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, R.308, P.309, T.310, Q.311, G.312, L.373, G.374, Q.375 Chain F: Y.103, R.104, D.106 Chain J: N.120, R.140 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain F Hydrogen bonds: D:T.310, D:R.247, D:D.250, D:R.283, D:I.285, F:R.104, F:D.106, D:G.312, D:G.312 NAG-NAG-BMA-MAN-MAN-MAN.5: 21 residues within 4Å: Chain A: N.120, R.140 Chain G: R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, R.308, P.309, T.310, Q.311, G.312, L.373, G.374, Q.375 Chain I: Y.103, R.104, D.106 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain I Hydrogen bonds: G:T.310, I:R.104, I:D.106, G:R.247, G:D.250, G:R.283, G:I.285, G:G.312, G:G.312 NAG-NAG-BMA-MAN-MAN-MAN.7: 21 residues within 4Å: Chain G: N.120, R.140 Chain J: R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, R.308, P.309, T.310, Q.311, G.312, L.373, G.374, Q.375 Chain L: Y.103, R.104, D.106 4 PLIP interactions: 2 interactions with chain J, 2 interactions with chain L Hydrogen bonds: J:T.310, L:R.104, L:D.106, J:R.247, J:D.250, J:R.283, J:I.285, J:G.312, J:G.312

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

NAG.2: 3 residues within 4Å: Chain A: F.3, N.5, N.154 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.5, A:N.154 NAG.4: 3 residues within 4Å: Chain D: F.3, N.5, N.154 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.5, D:N.154 NAG.6: 3 residues within 4Å: Chain G: F.3, N.5, N.154 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.5, G:N.154 NAG.8: 3 residues within 4Å: Chain J: F.3, N.5, N.154 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:N.5, J:N.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tulip, W.R. et al., N9 neuraminidase complexes with antibodies NC41 and NC10: empirical free energy calculations capture specificity trends observed with mutant binding data. Biochemistry (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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