SMTL ID : 3cye.1

Cyrstal structure of the native 1918 H1N1 neuraminidase from a crystal with lattice-translocation defects

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

2 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-MAN-MAN.1: 3 residues within 4Å: Chain B: N.64, T.66, I.354 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN.24: 3 residues within 4Å: Chain D: N.64, T.66, I.354 No protein-ligand interaction detected (PLIP)

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

NAG.2: 3 residues within 4Å: Chain A: N.64, T.66, I.354 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.354 Hydrogen bonds: A:N.64, A:T.66 NAG.25: 3 residues within 4Å: Chain C: N.64, T.66, I.354 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.354 Hydrogen bonds: C:N.64

10 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.3: 6 residues within 4Å: Chain A: D.212, G.216, D.242, G.260, N.262, G.263 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.212, A:G.216, A:D.242, A:G.260, A:N.262, H2O.2 CA.4: 4 residues within 4Å: Chain A: D.294, N.296, D.302, S.304 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.294, A:D.294, A:D.302, H2O.2, H2O.4 CA.5: 1 residues within 4Å: Ligands: CA.28 No protein-ligand interaction detected (PLIP) CA.15: 4 residues within 4Å: Chain B: D.294, N.296, D.302, S.304 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.294, B:D.294, B:D.302, H2O.16, H2O.19 CA.16: 6 residues within 4Å: Chain B: D.212, G.216, D.242, G.260, N.262, G.263 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.212, B:G.216, B:D.242, B:G.260, B:N.262, H2O.18 CA.26: 6 residues within 4Å: Chain C: D.212, G.216, D.242, G.260, N.262, G.263 6 PLIP interactions: 5 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.212, C:G.216, C:D.242, C:G.260, C:N.262, H2O.31 CA.27: 4 residues within 4Å: Chain C: D.294, N.296, D.302, S.304 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.294, C:D.294, C:D.302, H2O.31, H2O.33 CA.28: 1 residues within 4Å: Ligands: CA.5 No protein-ligand interaction detected (PLIP) CA.38: 4 residues within 4Å: Chain D: D.294, N.296, D.302, S.304 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.294, D:D.294, D:D.302, H2O.45, H2O.48 CA.39: 6 residues within 4Å: Chain D: D.212, G.216, D.242, G.260, N.262, G.263 6 PLIP interactions: 5 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.212, D:G.216, D:D.242, D:G.260, D:N.262, H2O.47

10 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 7 residues within 4Å: Chain A: Q.168, A.169, Y.171, L.187, N.188, A.189, P.190 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Q.168 Hydrogen bonds: A:Q.168, A:A.189 Water bridges: A:R.138, A:E.186, A:E.186 ACT.7: 6 residues within 4Å: Chain A: R.143, T.144, E.146, E.196 Ligands: ACT.8, PO4.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.146 Hydrogen bonds: A:E.146, A:E.146 ACT.8: 7 residues within 4Å: Chain A: R.70, W.97, S.98, I.141, R.143 Ligands: ACT.7, PO4.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.97, A:R.143 Water bridges: A:R.70 Salt bridges: A:R.70 ACT.17: 7 residues within 4Å: Chain B: R.70, W.97, S.98, R.143 Ligands: ACT.18, GOL.20, GOL.23 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.97, B:R.143 Water bridges: B:E.196 Salt bridges: B:R.70 ACT.18: 6 residues within 4Å: Chain B: T.144, E.146, E.196 Ligands: ACT.17, GOL.20, GOL.23 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.146 Hydrogen bonds: B:E.146, B:E.196 ACT.29: 7 residues within 4Å: Chain C: Q.168, A.169, Y.171, L.187, N.188, A.189, P.190 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Q.168 Hydrogen bonds: C:Q.168, C:A.189 Water bridges: C:R.138 ACT.30: 6 residues within 4Å: Chain C: R.143, T.144, E.146, E.196 Ligands: ACT.31, PO4.32 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:E.146 Hydrogen bonds: C:E.146, C:E.196 ACT.31: 7 residues within 4Å: Chain C: R.70, W.97, S.98, I.141, R.143 Ligands: ACT.30, PO4.32 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.97, C:R.143 Salt bridges: C:R.70 ACT.40: 7 residues within 4Å: Chain D: R.70, W.97, S.98, R.143 Ligands: ACT.41, GOL.43, GOL.46 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:W.97, D:R.143 Salt bridges: D:R.70 ACT.41: 6 residues within 4Å: Chain D: T.144, E.146, E.196 Ligands: ACT.40, GOL.43, GOL.46 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:E.146

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.9: 8 residues within 4Å: Chain A: R.143, S.165, E.195, E.196, R.211, N.213 Ligands: ACT.7, ACT.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.195, A:E.195 Water bridges: A:R.211 Salt bridges: A:R.211 PO4.32: 8 residues within 4Å: Chain C: R.143, S.165, E.195, E.196, R.211, N.213 Ligands: ACT.30, ACT.31 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.195, C:E.195 Water bridges: C:E.196, C:E.196, C:R.211 Salt bridges: C:R.211

20 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain A: Y.88, N.89, S.90 Chain D: P.80, E.83, N.89 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain A: P.11, I.12, Y.271, W.276, W.293 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain A: S.8, L.9, D.202, R.270, Y.271, D.272 Ligand excluded by PLIP GOL.13: 7 residues within 4Å: Chain A: P.80, E.83, N.89 Chain B: Y.88, N.89, S.90, R.91 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain A: G.249, T.250, T.301, D.302, S.303 Ligand excluded by PLIP GOL.19: 5 residues within 4Å: Chain B: P.11, I.12, Y.271, W.276, W.293 Ligand excluded by PLIP GOL.20: 9 residues within 4Å: Chain B: R.143, S.165, E.195, E.196, R.211, N.213, Y.320 Ligands: ACT.17, ACT.18 Ligand excluded by PLIP GOL.21: 5 residues within 4Å: Chain B: D.202, K.205, M.207, S.223, R.270 Ligand excluded by PLIP GOL.22: 7 residues within 4Å: Chain B: S.8, L.9, D.202, T.203, R.270, Y.271, D.272 Ligand excluded by PLIP GOL.23: 9 residues within 4Å: Chain B: R.36, E.37, L.52, D.69, R.74, W.97, Y.320 Ligands: ACT.17, ACT.18 Ligand excluded by PLIP GOL.33: 6 residues within 4Å: Chain B: P.80, E.83, N.89 Chain C: Y.88, N.89, S.90 Ligand excluded by PLIP GOL.34: 5 residues within 4Å: Chain C: P.11, I.12, Y.271, W.276, W.293 Ligand excluded by PLIP GOL.35: 6 residues within 4Å: Chain C: S.8, L.9, D.202, R.270, Y.271, D.272 Ligand excluded by PLIP GOL.36: 7 residues within 4Å: Chain C: P.80, E.83, N.89 Chain D: Y.88, N.89, S.90, R.91 Ligand excluded by PLIP GOL.37: 5 residues within 4Å: Chain C: G.249, T.250, T.301, D.302, S.303 Ligand excluded by PLIP GOL.42: 5 residues within 4Å: Chain D: P.11, I.12, Y.271, W.276, W.293 Ligand excluded by PLIP GOL.43: 9 residues within 4Å: Chain D: R.143, S.165, E.195, E.196, R.211, N.213, Y.320 Ligands: ACT.40, ACT.41 Ligand excluded by PLIP GOL.44: 5 residues within 4Å: Chain D: D.202, K.205, M.207, S.223, R.270 Ligand excluded by PLIP GOL.45: 7 residues within 4Å: Chain D: S.8, L.9, D.202, T.203, R.270, Y.271, D.272 Ligand excluded by PLIP GOL.46: 9 residues within 4Å: Chain D: R.36, E.37, L.52, D.69, R.74, W.97, Y.320 Ligands: ACT.40, ACT.41 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, X. et al., Structure determination of the 1918 H1N1 neuraminidase from a crystal with lattice-translocation defects. Acta Crystallogr.,Sect.D (2008)

Release Date

2008-08-05

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Neuraminidase