SMTL ID : 3d12.3 (2 other biounits)

Crystal Structures of Nipah Virus G Attachment Glycoprotein in Complex with its Receptor Ephrin-B3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.01 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- BMA- MAN: beta-D-mannopyranose-(1-3)-[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-BMA-MAN.1: 5 residues within 4Å: Chain A: T.124, V.125, L.130, N.131, Y.134 No protein-ligand interaction detected (PLIP)

1 x LXZ- NGA- GL0- BGC- GLC- BGC- GLC: beta-D-glucopyranose-(1-3)-[alpha-D-glucopyranose-(1-6)]beta-D-gulopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[beta-D-glucopyranose-(1-3)][alpha-D-glucopyranose-(1-6)]2-acetamido-2-deoxy-alpha-D-idopyranose

LXZ-NGA-GL0-BGC-GLC-BGC-GLC.2: 2 residues within 4Å: Chain A: N.322, N.354 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.322, B:R.84, A:N.354

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

NAG-NAG.3: 8 residues within 4Å: Chain A: Q.259, N.303, W.304, R.305, N.306 Ligands: SO4.8, SO4.10, SO4.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.259

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

NAG.4: 3 residues within 4Å: Chain A: N.203, S.205 Ligands: SO4.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.205

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 3 residues within 4Å: Chain A: R.227, S.230, H.231 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.231 Salt bridges: A:R.227 SO4.6: 3 residues within 4Å: Chain A: R.227, N.229 Chain B: A.69 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.229 SO4.7: 2 residues within 4Å: Chain A: N.206 Ligands: NAG.4 No protein-ligand interaction detected (PLIP) SO4.8: 2 residues within 4Å: Ligands: NAG-NAG.3, NAG-NAG.3 No protein-ligand interaction detected (PLIP) SO4.9: 4 residues within 4Å: Chain A: K.366, D.367, N.368, E.369 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.368, A:N.368, A:E.369 Salt bridges: A:K.366 SO4.10: 4 residues within 4Å: Chain A: D.293, N.303, R.305 Ligands: NAG-NAG.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.293, A:N.303 Salt bridges: A:R.305 SO4.11: 5 residues within 4Å: Chain A: D.258, Q.259, R.260 Ligands: NAG-NAG.3, SO4.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.260 SO4.12: 7 residues within 4Å: Chain A: Y.202, N.206, P.208, D.258, R.260, L.261 Ligands: SO4.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.261 SO4.13: 4 residues within 4Å: Chain A: K.421, P.423, E.424, Q.425 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.424, A:Q.425 Salt bridges: A:K.421 SO4.14: 6 residues within 4Å: Chain B: E.57, G.58, A.59, R.62, H.105, D.106 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.59, B:D.106, B:D.106 Salt bridges: B:R.62, B:H.105 SO4.15: 3 residues within 4Å: Chain B: A.59, R.62, R.63 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.63 Salt bridges: B:R.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, K. et al., Host cell recognition by the henipaviruses: crystal structures of the Nipah G attachment glycoprotein and its complex with ephrin-B3. Proc.Natl.Acad.Sci.USA (2008)

Release Date

2008-08-19

Peptides

Hemagglutinin-neuraminidase: A
Ephrin-B3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hemagglutinin-neuraminidase

Ephrin-B3

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