SMTL ID : 3d12.2 (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- 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.1: 4 residues within 4Å: Chain A: V.125, L.130, N.131, Y.134 No protein-ligand interaction detected (PLIP)

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.2: 5 residues within 4Å: Chain A: R.320, F.321, N.322, N.354 Chain B: R.84 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.354, B:R.84 Water bridges: A:R.320, A:R.320, B:R.84

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: 6 residues within 4Å: Chain A: L.295, N.303, W.304, N.306 Ligands: SO4.7, SO4.9 No protein-ligand interaction detected (PLIP)

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: SO4.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.205

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

SO4.5: 4 residues within 4Å: Chain A: T.133, 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: 2 residues within 4Å: Chain A: N.206 Ligands: NAG.4 No protein-ligand interaction detected (PLIP) SO4.7: 2 residues within 4Å: Ligands: NAG-NAG.3, NAG-NAG.3 No protein-ligand interaction detected (PLIP) SO4.8: 4 residues within 4Å: Chain A: K.366, D.367, N.368, E.369 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.368, A:N.368 Salt bridges: A:K.366 SO4.9: 3 residues within 4Å: Chain A: R.305, W.344 Ligands: NAG-NAG.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.305 SO4.10: 4 residues within 4Å: Chain A: D.258, Q.259, R.260 Ligands: SO4.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.259, A:R.260 SO4.11: 9 residues within 4Å: Chain A: Y.202, N.206, P.208, C.220, D.258, R.260, L.261, W.285 Ligands: SO4.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.202, A:L.261 SO4.12: 4 residues within 4Å: Chain A: K.421, P.423, E.424, Q.425 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.424, A:E.424, A:Q.425 Salt bridges: A:K.421 SO4.13: 6 residues within 4Å: Chain A: G.152, G.153, G.154, Y.155, N.156, Q.157 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.152, A:G.153, A:G.154, A:Y.155, A:N.156, A:N.156, A:Q.157 SO4.14: 3 residues within 4Å: Chain A: R.143, G.154, Y.155 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.143 SO4.15: 2 residues within 4Å: Chain B: T.130, R.131 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.130 Salt bridges: B:R.131

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
D

B
E

Hemagglutinin-neuraminidase

Ephrin-B3

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