SMTL ID : 1nmc.1 (1 other biounit)

COMPLEX BETWEEN NC10 ANTI-INFLUENZA VIRUS NEURAMINIDASE SINGLE CHAIN ANTIBODY WITH A 15 RESIDUE LINKER AND INFLUENZA VIRUS NEURAMINIDASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 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: 23 residues within 4Å: Chain A: N.120, R.140 Chain J: R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, Q.313, F.372, L.373, G.374, Q.375 Chain K: R.104, D.106 Ligands: MAN.2 6 PLIP interactions: 4 interactions with chain J, 2 interactions with chain K Hydrogen bonds: J:T.310, J:R.247, J:R.247, J:D.250, J:I.285, K:R.104, K:D.106, J:G.312 Water bridges: J:Q.313, J:Q.311, J:G.312 Hydrophobic interactions: J:F.372 NAG-NAG-BMA-MAN-MAN-MAN.6: 23 residues within 4Å: Chain D: N.120, R.140 Chain G: R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, Q.313, F.372, L.373, G.374, Q.375 Chain H: R.104, D.106 Ligands: MAN.7 6 PLIP interactions: 4 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:T.310, G:R.247, G:R.247, G:D.250, G:I.285, H:R.104, H:D.106, G:G.312 Water bridges: G:Q.313, G:Q.311, G:G.312 Hydrophobic interactions: G:F.372 NAG-NAG-BMA-MAN-MAN-MAN.11: 23 residues within 4Å: Chain A: R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, Q.313, F.372, L.373, G.374, Q.375 Chain B: R.104, D.106 Chain G: N.120, R.140 Ligands: MAN.12 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.310, A:R.247, A:R.247, A:D.250, A:I.285, B:R.104, B:D.106, A:G.312 Water bridges: A:Q.313, A:Q.311, A:G.312 Hydrophobic interactions: A:F.372 NAG-NAG-BMA-MAN-MAN-MAN.16: 23 residues within 4Å: Chain D: R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, Q.313, F.372, L.373, G.374, Q.375 Chain E: R.104, D.106 Chain J: N.120, R.140 Ligands: MAN.17 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:T.310, E:R.104, E:D.106, D:R.247, D:R.247, D:D.250, D:I.285, D:G.312 Water bridges: D:Q.313, D:Q.311, D:G.312 Hydrophobic interactions: D:F.372

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

MAN.2: 2 residues within 4Å: Chain J: T.310 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.1 No protein-ligand interaction detected (PLIP) MAN.7: 2 residues within 4Å: Chain G: T.310 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.6 No protein-ligand interaction detected (PLIP) MAN.12: 2 residues within 4Å: Chain A: T.310 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.11 No protein-ligand interaction detected (PLIP) MAN.17: 2 residues within 4Å: Chain D: T.310 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.16 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain A: N.65, W.357 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.65, A:W.357 NAG.4: 4 residues within 4Å: Chain A: D.2, F.3, N.5, N.154 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.2 Hydrogen bonds: A:D.2, A:F.3 NAG.8: 2 residues within 4Å: Chain D: N.65, W.357 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.65, D:W.357 NAG.9: 4 residues within 4Å: Chain D: D.2, F.3, N.5, N.154 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:D.2 Hydrogen bonds: D:D.2, D:F.3 NAG.13: 2 residues within 4Å: Chain G: N.65, W.357 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.65, G:W.357 NAG.14: 4 residues within 4Å: Chain G: D.2, F.3, N.5, N.154 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:D.2 Hydrogen bonds: G:D.2, G:F.3 NAG.18: 2 residues within 4Å: Chain J: N.65, W.357 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:N.65, J:W.357 NAG.19: 4 residues within 4Å: Chain J: D.2, F.3, N.5, N.154 3 PLIP interactions: 3 interactions with chain J Hydrophobic interactions: J:D.2 Hydrogen bonds: J:D.2, J:F.3

4 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: N.214, G.217, D.244, N.266 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.217, A:N.266, H2O.3 CA.10: 4 residues within 4Å: Chain D: N.214, G.217, D.244, N.266 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:G.217, D:N.266, H2O.6 CA.15: 4 residues within 4Å: Chain G: N.214, G.217, D.244, N.266 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:G.217, G:N.266, H2O.10 CA.20: 4 residues within 4Å: Chain J: N.214, G.217, D.244, N.266 3 PLIP interactions: 2 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:G.217, J:N.266, H2O.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malby, R.L. et al., Three-dimensional structures of single-chain Fv-neuraminidase complexes. J.Mol.Biol. (1998)

Release Date

1998-09-23

Peptides

NEURAMINIDASE: ADGJ
SINGLE CHAIN ANTIBODY: BEHK
SINGLE CHAIN ANTIBODY: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
N

D
N

G
N

J
N

B
H

E
H

H
H

K
H

C
L

F
L

I
L

L
L

NEURAMINIDASE

SINGLE CHAIN ANTIBODY

SINGLE CHAIN ANTIBODY

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