SMTL ID : 1ncd.1

REFINED CRYSTAL STRUCTURE OF THE INFLUENZA VIRUS N9 NEURAMINIDASE-NC41 FAB COMPLEX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 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: 22 residues within 4Å: Chain A: N.120, N.121, R.141 Chain G: V.242, R.248, N.250, D.251, R.284, I.286, I.288, E.295, L.297, K.309, P.310, T.311, Q.312, G.313, Q.314, F.373, L.374, G.375, Q.376 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain I Hydrogen bonds: G:T.311, G:R.248, G:D.251, G:I.286, I:Y.32, G:G.313, G:G.313 Water bridges: G:Q.314, G:Q.314, G:Q.314 Hydrophobic interactions: G:F.373 NAG-NAG-BMA-MAN-MAN-MAN.5: 22 residues within 4Å: Chain A: V.242, R.248, N.250, D.251, R.284, I.286, I.288, E.295, L.297, K.309, P.310, T.311, Q.312, G.313, Q.314, F.373, L.374, G.375, Q.376 Chain D: N.120, N.121, R.141 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:T.311, A:R.248, A:D.251, A:I.286, C:Y.32, A:G.313, A:G.313 Water bridges: A:Q.314, A:Q.314, A:Q.314 Hydrophobic interactions: A:F.373 NAG-NAG-BMA-MAN-MAN-MAN.9: 22 residues within 4Å: Chain G: N.120, N.121, R.141 Chain J: V.242, R.248, N.250, D.251, R.284, I.286, I.288, E.295, L.297, K.309, P.310, T.311, Q.312, G.313, Q.314, F.373, L.374, G.375, Q.376 5 PLIP interactions: 4 interactions with chain J, 1 interactions with chain L Hydrogen bonds: J:T.311, J:R.248, J:D.251, J:I.286, L:Y.32, J:G.313, J:G.313 Water bridges: J:Q.314, J:Q.314, J:Q.314 Hydrophobic interactions: J:F.373 NAG-NAG-BMA-MAN-MAN-MAN.13: 22 residues within 4Å: Chain D: V.242, R.248, N.250, D.251, R.284, I.286, I.288, E.295, L.297, K.309, P.310, T.311, Q.312, G.313, Q.314, F.373, L.374, G.375, Q.376 Chain J: N.120, N.121, R.141 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:T.311, D:R.248, D:D.251, D:I.286, F:Y.32, D:G.313, D:G.313 Water bridges: D:Q.314, D:Q.314, D:Q.314 Hydrophobic interactions: D:F.373

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.2: 2 residues within 4Å: Chain A: N.66, W.358 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain D: N.66, W.358 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain G: N.66, W.358 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain J: N.66, W.358 No protein-ligand interaction detected (PLIP)

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

NAG.3: 4 residues within 4Å: Chain A: E.3, N.6, Q.154, N.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.6, A:Q.154 NAG.7: 4 residues within 4Å: Chain D: E.3, N.6, Q.154, N.155 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.6, D:Q.154 NAG.11: 4 residues within 4Å: Chain G: E.3, N.6, Q.154, N.155 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.6, G:Q.154 NAG.15: 4 residues within 4Å: Chain J: E.3, N.6, Q.154, N.155 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:N.6, J:Q.154

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 7 residues within 4Å: Chain A: D.214, N.215, G.218, S.219, D.245, N.264, N.267 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:G.218, A:N.264, A:N.267 CA.8: 7 residues within 4Å: Chain D: D.214, N.215, G.218, S.219, D.245, N.264, N.267 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:G.218, D:N.264, D:N.267 CA.12: 7 residues within 4Å: Chain G: D.214, N.215, G.218, S.219, D.245, N.264, N.267 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:G.218, G:N.264, G:N.267 CA.16: 7 residues within 4Å: Chain J: D.214, N.215, G.218, S.219, D.245, N.264, N.267 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:G.218, J:N.264, J:N.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tulip, W.R. et al., Refined crystal structure of the influenza virus N9 neuraminidase-NC41 Fab complex. J.Mol.Biol. (1992)

Release Date

1994-01-31

Peptides

INFLUENZA A SUBTYPE N9 NEURAMINIDASE: ADGJ
IGG2A-KAPPA NC41 FAB (LIGHT CHAIN): BEHK
IGG2A-KAPPA NC41 FAB (HEAVY CHAIN): 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

INFLUENZA A SUBTYPE N9 NEURAMINIDASE

IGG2A-KAPPA NC41 FAB (LIGHT CHAIN)

IGG2A-KAPPA NC41 FAB (HEAVY CHAIN)

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