SMTL ID : 3d12.1 (2 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.01 Å

Oligo State

hetero-2-2-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: 9 residues within 4Å: Chain A: T.124, V.125, L.130, N.131, Y.134 Chain D: Q.15, L.129, T.130 Ligands: SO4.30 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.15

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

2 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 NAG-NAG.18: 6 residues within 4Å: Chain C: L.295, N.303, W.304, N.306 Ligands: SO4.22, SO4.24 No protein-ligand interaction detected (PLIP)

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

NAG.4: 4 residues within 4Å: Chain A: N.203, S.205 Ligands: SO4.7, NAG-NAG-BMA-BGC-MAN.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.205 NAG.19: 3 residues within 4Å: Chain C: N.203, S.205 Ligands: SO4.21 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.205

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

SO4.5: 5 residues within 4Å: Chain A: R.227, S.230, H.231 Chain D: R.62, R.63 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: R.227, N.229 Chain B: A.69 Chain D: A.59, R.62 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: N.206 Ligands: NAG.4 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Ligands: NAG-NAG.3, NAG-NAG.3 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: K.366, D.367, N.368, E.369 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain A: D.293, N.303, R.305 Ligands: NAG-NAG.3 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain A: D.258, Q.259, R.260 Ligands: NAG-NAG.3, SO4.12 Ligand excluded by PLIP SO4.12: 7 residues within 4Å: Chain A: Y.202, N.206, P.208, D.258, R.260, L.261 Ligands: SO4.11 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain A: K.421, P.423, E.424, Q.425 Ligand excluded by PLIP SO4.14: 6 residues within 4Å: Chain B: E.57, G.58, A.59, R.62, H.105, D.106 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain B: A.59, R.62, R.63 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain C: T.133, R.227, S.230, H.231 Ligand excluded by PLIP SO4.21: 2 residues within 4Å: Chain C: N.206 Ligands: NAG.19 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Ligands: NAG-NAG.18, NAG-NAG.18 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain C: K.366, D.367, N.368, E.369 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain C: R.305, W.344 Ligands: NAG-NAG.18 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain C: D.258, Q.259, R.260 Ligands: SO4.26 Ligand excluded by PLIP SO4.26: 9 residues within 4Å: Chain C: Y.202, N.206, P.208, C.220, D.258, R.260, L.261, W.285 Ligands: SO4.25 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain C: K.421, P.423, E.424, Q.425 Ligand excluded by PLIP SO4.28: 6 residues within 4Å: Chain C: G.152, G.153, G.154, Y.155, N.156, Q.157 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain C: R.143, G.154, Y.155 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain D: T.130, R.131 Ligands: NAG-NAG-BMA-BMA-MAN.1 Ligand excluded by PLIP

1 x NAG- NAG- BMA- BGC- MAN: beta-D-glucopyranose-(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-BGC-MAN.16: 8 residues within 4Å: Chain A: Y.202, D.204, R.221 Chain C: V.125, L.130, N.131, Y.134 Ligands: NAG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.204

1 x LXB- NGZ- GL0- BGC- GLC- BGC- GXL: beta-D-glucopyranose-(1-3)-[alpha-D-glucopyranose-(1-6)]beta-D-gulopyranose-(1-4)-2-acetamido-2-deoxy-alpha-L-glucopyranose-(1-4)-[beta-D-glucopyranose-(1-3)][alpha-L-galactopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-gulopyranose

LXB-NGZ-GL0-BGC-GLC-BGC-GXL.17: 5 residues within 4Å: Chain C: R.320, F.321, N.322, N.354 Chain D: R.84 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:N.354, D:R.84 Water bridges: C:R.320, C:R.320, D:R.84

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: AC
Ephrin-B3: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

B
B

D
E

Hemagglutinin-neuraminidase

Ephrin-B3

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