SMTL ID : 6pze.1 (1 other biounit)

Crystal structure of human NA-45 Fab in complex with neuraminidase Y169aH mutant from A/Shanghai/2/2013 (H7N9)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-4-4-4-mer

Ligands

4 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN.1: 18 residues within 4Å: Chain A: N.124, N.125 Chain C: R.252, N.254, D.255, R.288, I.290, T.292, E.299, L.301, P.314, I.315, Q.316, G.317, F.377, L.378, G.379, Q.380 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.377 Hydrogen bonds: C:G.317 Water bridges: C:Q.316, C:G.317 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.4: 18 residues within 4Å: Chain B: N.124, N.125 Chain D: R.252, N.254, D.255, R.288, I.290, T.292, E.299, L.301, P.314, I.315, Q.316, G.317, F.377, L.378, G.379, Q.380 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.377 Hydrogen bonds: D:G.317 Water bridges: D:Q.316, D:G.317 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.7: 18 residues within 4Å: Chain B: R.252, N.254, D.255, R.288, I.290, T.292, E.299, L.301, P.314, I.315, Q.316, G.317, F.377, L.378, G.379, Q.380 Chain C: N.124, N.125 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.377 Hydrogen bonds: B:G.317 Water bridges: B:Q.316, B:G.317 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.10: 18 residues within 4Å: Chain A: R.252, N.254, D.255, R.288, I.290, T.292, E.299, L.301, P.314, I.315, Q.316, G.317, F.377, L.378, G.379, Q.380 Chain D: N.124, N.125 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.377 Hydrogen bonds: A:G.317 Water bridges: A:Q.316, A:G.317

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: 4 residues within 4Å: Chain A: N.70 Chain C: K.388, E.390, Y.391 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.390, C:E.390 NAG-NAG.5: 4 residues within 4Å: Chain B: N.70 Chain D: K.388, E.390, Y.391 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.390, D:E.390 NAG-NAG.8: 4 residues within 4Å: Chain B: K.388, E.390, Y.391 Chain C: N.70 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.390, B:E.390 NAG-NAG.11: 4 residues within 4Å: Chain A: K.388, E.390, Y.391 Chain D: N.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.390, A:E.390

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.218, G.222, D.249, N.271, G.272 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.218, A:G.222, A:D.249, H2O.2, H2O.6 CA.6: 5 residues within 4Å: Chain B: D.218, G.222, D.249, N.271, G.272 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.218, B:G.222, B:D.249, H2O.16, H2O.20 CA.9: 5 residues within 4Å: Chain C: D.218, G.222, D.249, N.271, G.272 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.218, C:G.222, C:D.249, H2O.30, H2O.34 CA.12: 5 residues within 4Å: Chain D: D.218, G.222, D.249, N.271, G.272 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.218, D:G.222, D:D.249, H2O.45, H2O.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, X. et al., Structural Basis of Protection against H7N9 Influenza Virus by Human Anti-N9 Neuraminidase Antibodies. Cell Host Microbe (2019)

Release Date

2019-12-04

Peptides

Neuraminidase: ABCD
NA-45 FAB LIGHT CHAIN: EGIK
NA-45 FAB HEAVY CHAIN: FHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
L

G
L

I
L

K
L

F
H

H
H

J
H

L
H

Neuraminidase

NA-45 FAB LIGHT CHAIN

NA-45 FAB HEAVY CHAIN

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