SMTL ID : 3nss.1

The 2009 pandemic H1N1 neuraminidase N1 lacks the 150-cavity in its active sites

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 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

NAG-NAG-MAN-MAN.1: 4 residues within 4Å: Chain A: K.62, N.65, I.355, I.386 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN.14: 4 residues within 4Å: Chain C: K.62, N.65, I.355, I.386 No protein-ligand interaction detected (PLIP)

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

NAG.2: 2 residues within 4Å: Chain A: A.5, N.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.7 NAG.9: 1 residues within 4Å: Chain B: N.65 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.65 Water bridges: B:N.65, A:E.381 NAG.10: 1 residues within 4Å: Chain B: N.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.7 NAG.15: 2 residues within 4Å: Chain C: A.5, N.7 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.7 NAG.22: 1 residues within 4Å: Chain D: N.65 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.65 Water bridges: D:N.65 NAG.23: 1 residues within 4Å: Chain D: N.7 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.7

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

CA.3: 5 residues within 4Å: Chain A: D.213, G.217, D.243, G.261, N.263 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.213, A:G.217, A:D.243, A:G.261, A:N.263, H2O.2 CA.4: 4 residues within 4Å: Chain A: D.295, N.297, D.303, N.305 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.295, A:D.303, A:N.305, H2O.3, H2O.5 CA.5: 1 residues within 4Å: Ligands: CA.18 No protein-ligand interaction detected (PLIP) CA.11: 5 residues within 4Å: Chain B: D.213, G.217, D.243, G.261, N.263 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.213, B:G.217, B:D.243, B:G.261, B:N.263, H2O.18 CA.12: 4 residues within 4Å: Chain B: D.295, N.297, D.303, N.305 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.295, B:D.303, B:N.305, H2O.19, H2O.24 CA.16: 5 residues within 4Å: Chain C: D.213, G.217, D.243, G.261, N.263 6 PLIP interactions: 5 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.213, C:G.217, C:D.243, C:G.261, C:N.263, H2O.36 CA.17: 4 residues within 4Å: Chain C: D.295, N.297, D.303, N.305 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.295, C:D.303, C:N.305, H2O.37, H2O.40 CA.18: 1 residues within 4Å: Ligands: CA.5 No protein-ligand interaction detected (PLIP) CA.24: 5 residues within 4Å: Chain D: D.213, G.217, D.243, G.261, N.263 6 PLIP interactions: 5 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.213, D:G.217, D:D.243, D:G.261, D:N.263, H2O.52 CA.25: 4 residues within 4Å: Chain D: D.295, N.297, D.303, N.305 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.295, D:D.303, D:N.305, H2O.53, H2O.58

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

ACT.6: 4 residues within 4Å: Chain A: S.166, E.196, E.197, R.212 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.197 Salt bridges: A:R.212 ACT.7: 4 residues within 4Å: Chain A: P.12, V.13, Y.272, W.277 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.272 Hydrogen bonds: A:V.13 ACT.8: 3 residues within 4Å: Chain A: N.192, G.255, P.256 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.192 Water bridges: A:Y.193 ACT.13: 4 residues within 4Å: Chain B: P.12, V.13, W.277, W.294 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.13 ACT.19: 4 residues within 4Å: Chain C: S.166, E.196, E.197, R.212 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.197 Water bridges: C:Y.321 Salt bridges: C:R.212 ACT.20: 4 residues within 4Å: Chain C: P.12, V.13, Y.272, W.277 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.272 Hydrogen bonds: C:V.13 ACT.21: 3 residues within 4Å: Chain C: N.192, G.255, P.256 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.192 Water bridges: C:Y.193 ACT.26: 4 residues within 4Å: Chain D: P.12, V.13, W.277, W.294 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Q. et al., The 2009 pandemic H1N1 neuraminidase N1 lacks the 150-cavity in its active site. Nat.Struct.Mol.Biol. (2010)

Release Date

2010-09-22

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Neuraminidase

Related Entries With Identical Sequence