SMTL ID : 1usr.1

Newcastle disease virus hemagglutinin-neuraminidase: Evidence for a second sialic acid binding site and implications for fusion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

1 x WIA- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-methyl 6-thio-beta-D-galactopyranoside(Non-covalent)

WIA-SIA.1: 9 residues within 4Å: Chain A: A.32, F.33, T.392, R.393, V.394, S.395, S.396 Chain B: T.45, G.46 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.32, A:F.33 Hydrogen bonds: A:F.33, A:R.393, A:R.393, A:R.393, A:S.395, A:S.396, B:G.46 Water bridges: A:S.397, B:S.47 Salt bridges: A:R.393

2 x DAN: 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID(Non-covalent)

DAN.2: 11 residues within 4Å: Chain A: R.51, I.52, E.135, Y.176, Y.194, R.240, E.278, R.293, V.343, R.375, Y.403 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.176 Hydrogen bonds: A:Y.194, A:Y.194, A:R.240, A:E.278, A:R.293 Water bridges: A:Y.139, A:R.240, A:E.278, A:E.278, A:R.293, A:S.295 Salt bridges: A:R.51, A:R.293, A:R.375 DAN.5: 12 residues within 4Å: Chain B: R.51, I.52, E.135, Y.176, Y.194, R.240, F.241, E.278, R.293, V.343, R.375, Y.403 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.52, B:Y.176 Hydrogen bonds: B:Y.194, B:Y.194, B:R.240, B:E.278, B:R.293 Water bridges: B:E.135, B:E.135, B:Y.139, B:Y.139, B:R.293, B:R.293, B:S.295 Salt bridges: B:R.51, B:R.293, B:R.375

2 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)

NDG.3: 3 residues within 4Å: Chain A: Y.356, N.358, T.360 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.358, A:T.360, A:T.360 Water bridges: A:N.21, A:N.358 NDG.6: 3 residues within 4Å: Chain B: Y.356, N.358, T.360 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.358, B:T.360, B:T.360

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: E.133, D.138, S.141, V.143, V.173 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.138, A:S.141, A:S.141, A:V.143, A:V.173 CA.8: 4 residues within 4Å: Chain B: D.138, S.141, V.143, V.173 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.138, B:D.138, B:V.143, B:V.173, H2O.24

1 x SIA: N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA.7: 9 residues within 4Å: Chain A: T.45, G.46 Chain B: A.32, F.33, T.392, R.393, V.394, S.395, S.396 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:G.46, B:F.33, B:R.393, B:R.393, B:S.396 Water bridges: A:S.47, B:S.395, B:S.395, B:S.397 Hydrophobic interactions: B:A.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zaitsev, V. et al., Second Sialic Acid Binding Site in Newcastle Disease Virus Hemagglutinin-Neuraminidase: Implications for Fusion. J.Virol. (2004)

Release Date

2004-01-02

Peptides

HEMAGGLUTININ-NEURAMINIDASE GLYCOPROTEIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HEMAGGLUTININ-NEURAMINIDASE GLYCOPROTEIN

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