SMTL ID : 6pzd.1

Crystal structure of the neuraminidase stabilization mutant Y169aH from A/Shanghai/2/2013 (H7N9)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.12 Å

Oligo State

homo-tetramer

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: 23 residues within 4Å: Chain A: N.124, N.125, R.145 Chain C: V.246, R.252, N.254, D.255, R.288, I.290, T.292, E.299, L.301, K.313, P.314, I.315, Q.316, G.317, Q.318, F.377, L.378, G.379, Q.380 Ligands: EDO.21 5 PLIP interactions: 5 interactions with chain C Water bridges: C:P.314, C:Q.316, C:Q.316, C:Q.380 Hydrophobic interactions: C:F.377 Hydrogen bonds: C:G.317 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.10: 23 residues within 4Å: Chain B: N.124, N.125, R.145 Chain D: V.246, R.252, N.254, D.255, R.288, I.290, T.292, E.299, L.301, K.313, P.314, I.315, Q.316, G.317, Q.318, F.377, L.378, G.379, Q.380 Ligands: EDO.30 5 PLIP interactions: 5 interactions with chain D Water bridges: D:P.314, D:Q.316, D:Q.316, D:Q.380 Hydrophobic interactions: D:F.377 Hydrogen bonds: D:G.317 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.19: 23 residues within 4Å: Chain B: V.246, R.252, N.254, D.255, R.288, I.290, T.292, E.299, L.301, K.313, P.314, I.315, Q.316, G.317, Q.318, F.377, L.378, G.379, Q.380 Chain C: N.124, N.125, R.145 Ligands: EDO.12 5 PLIP interactions: 5 interactions with chain B Water bridges: B:P.314, B:Q.316, B:Q.316, B:Q.380 Hydrophobic interactions: B:F.377 Hydrogen bonds: B:G.317 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.28: 23 residues within 4Å: Chain A: V.246, R.252, N.254, D.255, R.288, I.290, T.292, E.299, L.301, K.313, P.314, I.315, Q.316, G.317, Q.318, F.377, L.378, G.379, Q.380 Chain D: N.124, N.125, R.145 Ligands: EDO.3 5 PLIP interactions: 5 interactions with chain A Water bridges: A:P.314, A:Q.316, A:Q.316, A:Q.380 Hydrophobic interactions: A:F.377 Hydrogen bonds: A:G.317

20 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 8 residues within 4Å: Chain A: C.16, A.338, E.339, G.340, D.341, C.342, Y.343, R.344 Ligand excluded by PLIP EDO.3: 9 residues within 4Å: Chain A: E.299, L.301, G.317, Q.318, T.319, Q.380 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.28, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.28, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.28 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: T.319, L.322, Q.380, W.381, N.382 Chain D: P.122 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: D.75, R.76, W.103, S.104, I.147, R.149, E.152 Ligands: EDO.6 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: R.149, A.171, E.201, E.202, R.217, N.219, Y.329 Ligands: EDO.5 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain B: C.16, A.338, E.339, G.340, D.341, C.342, Y.343, R.344 Ligand excluded by PLIP EDO.12: 9 residues within 4Å: Chain B: E.299, L.301, G.317, Q.318, T.319, Q.380 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.19, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.19, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.19 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain B: T.319, L.322, Q.380, W.381, N.382 Chain C: P.122 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain B: D.75, R.76, W.103, S.104, I.147, R.149, E.152 Ligands: EDO.15 Ligand excluded by PLIP EDO.15: 8 residues within 4Å: Chain B: R.149, A.171, E.201, E.202, R.217, N.219, Y.329 Ligands: EDO.14 Ligand excluded by PLIP EDO.20: 8 residues within 4Å: Chain C: C.16, A.338, E.339, G.340, D.341, C.342, Y.343, R.344 Ligand excluded by PLIP EDO.21: 9 residues within 4Å: Chain C: E.299, L.301, G.317, Q.318, T.319, Q.380 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain A: P.122 Chain C: T.319, L.322, Q.380, W.381, N.382 Ligand excluded by PLIP EDO.23: 8 residues within 4Å: Chain C: D.75, R.76, W.103, S.104, I.147, R.149, E.152 Ligands: EDO.24 Ligand excluded by PLIP EDO.24: 8 residues within 4Å: Chain C: R.149, A.171, E.201, E.202, R.217, N.219, Y.329 Ligands: EDO.23 Ligand excluded by PLIP EDO.29: 8 residues within 4Å: Chain D: C.16, A.338, E.339, G.340, D.341, C.342, Y.343, R.344 Ligand excluded by PLIP EDO.30: 9 residues within 4Å: Chain D: E.299, L.301, G.317, Q.318, T.319, Q.380 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.10, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.10, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.10 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain B: P.122 Chain D: T.319, L.322, Q.380, W.381, N.382 Ligand excluded by PLIP EDO.32: 8 residues within 4Å: Chain D: D.75, R.76, W.103, S.104, I.147, R.149, E.152 Ligands: EDO.33 Ligand excluded by PLIP EDO.33: 8 residues within 4Å: Chain D: R.149, A.171, E.201, E.202, R.217, N.219, Y.329 Ligands: EDO.32 Ligand excluded by PLIP

4 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.7: 10 residues within 4Å: Chain A: L.11, T.12, H.158, E.208, R.209, T.210, G.211, D.231, P.232, V.233 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.209 Water bridges: A:T.12 MES.16: 10 residues within 4Å: Chain B: L.11, T.12, H.158, E.208, R.209, T.210, G.211, D.231, P.232, V.233 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.209 Water bridges: B:T.12 MES.25: 10 residues within 4Å: Chain C: L.11, T.12, H.158, E.208, R.209, T.210, G.211, D.231, P.232, V.233 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.209 Water bridges: C:T.12 MES.34: 10 residues within 4Å: Chain D: L.11, T.12, H.158, E.208, R.209, T.210, G.211, D.231, P.232, V.233 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.209 Water bridges: D:T.12

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

NAG.8: 2 residues within 4Å: Chain A: N.70, W.362 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.70 Water bridges: A:W.362, A:W.362, C:Y.391 NAG.17: 2 residues within 4Å: Chain B: N.70, W.362 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B Water bridges: D:Y.391, B:W.362, B:W.362 Hydrogen bonds: B:N.70 NAG.26: 2 residues within 4Å: Chain C: N.70, W.362 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Water bridges: B:Y.391, C:W.362, C:W.362 Hydrogen bonds: C:N.70 NAG.35: 2 residues within 4Å: Chain D: N.70, W.362 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:N.70 Water bridges: D:W.362, D:W.362, A:Y.391

4 x CA: CALCIUM ION(Non-covalent)

CA.9: 7 residues within 4Å: Chain A: D.218, N.219, G.222, S.223, D.249, N.271, G.272 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.218, A:G.222, A:D.249, A:N.271, H2O.7, H2O.13 CA.18: 7 residues within 4Å: Chain B: D.218, N.219, G.222, S.223, D.249, N.271, G.272 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.218, B:G.222, B:D.249, B:N.271, H2O.29, H2O.35 CA.27: 7 residues within 4Å: Chain C: D.218, N.219, G.222, S.223, D.249, N.271, G.272 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.218, C:G.222, C:D.249, C:N.271, H2O.52, H2O.58 CA.36: 7 residues within 4Å: Chain D: D.218, N.219, G.222, S.223, D.249, N.271, G.272 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.218, D:G.222, D:D.249, D:N.271, H2O.75, H2O.81

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Neuraminidase

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