SMTL ID : 6vy6.1

Crystal structure of Hendra receptor binding protein head domain in complex with human neutralizing antibody HENV-26

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: N.218, K.220, S.221, H.222 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.218, A:H.222 Water bridges: A:S.123, A:Y.223 SO4.2: 5 residues within 4Å: Chain A: N.262, S.263, L.264, G.265 Ligands: MPD.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.262, A:N.262, A:L.264, A:G.265 SO4.3: 2 residues within 4Å: Chain A: V.156, R.158 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.158 SO4.9: 3 residues within 4Å: Chain B: T.69, Q.82, N.84 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.69, B:T.69, B:N.84 SO4.11: 1 residues within 4Å: Chain C: S.189 No protein-ligand interaction detected (PLIP)

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 11 residues within 4Å: Chain A: N.262, S.263, L.264, F.328, L.329, I.330, C.381, F.382, L.383, I.388 Ligands: SO4.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.328, A:L.383, A:I.388 Hydrogen bonds: A:L.264

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

NAG.5: 7 residues within 4Å: Chain A: R.311, F.312, N.345 Chain C: S.92, S.93, S.94, D.95 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.311, A:F.312, A:N.345, A:N.345 NAG.6: 3 residues within 4Å: Chain A: V.116, N.122, S.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.122, A:S.125 NAG.7: 6 residues within 4Å: Chain A: T.177, Y.179, K.231, N.233, S.235, L.236 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.231, A:N.233 Water bridges: A:T.177, A:S.235 NAG.8: 4 residues within 4Å: Chain A: Q.294, W.295, R.296, N.297 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.294 Hydrogen bonds: A:Q.294, A:W.295, A:N.297 Water bridges: A:N.297

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 3 residues within 4Å: Chain B: F.27, T.28, F.32 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.12: 1 residues within 4Å: Chain C: H.190 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, J. et al., Potent Henipavirus Neutralization by Antibodies Recognizing Diverse Sites on Hendra and Nipah Virus Receptor Binding Protein. Cell (2020)

Release Date

2021-01-06

Peptides

receptor binding protein: A
Anti-Hendra receptor binding protein antibody HENV-26 Fab heavy chain: B
Anti-Hendra receptor binding protein antibody HENV-26 Fab light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

receptor binding protein

Anti-Hendra receptor binding protein antibody HENV-26 Fab heavy chain

Anti-Hendra receptor binding protein antibody HENV-26 Fab light chain

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