SMTL ID : 6vy4.1

Crystal structure of Hendra receptor binding protein head domain in complex with human neutralizing antibody HENV-32

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: K.357, D.358, N.359 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.358, A:D.358, A:N.359, A:N.359 Water bridges: A:K.357, A:K.357 Salt bridges: A:K.357 SO4.8: 3 residues within 4Å: Chain B: R.28, K.62, Q.63 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.63 Salt bridges: B:R.28, B:K.62 SO4.9: 5 residues within 4Å: Chain B: L.72, D.73, R.74 Chain C: I.28 Chain E: R.62 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain B Salt bridges: E:R.62, B:R.74 SO4.16: 6 residues within 4Å: Chain C: Q.1, V.2, G.27, R.98, R.100 Chain E: R.62 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:V.2 Salt bridges: C:R.98, C:R.100, E:R.62 SO4.17: 5 residues within 4Å: Chain E: Q.1, V.2, G.26, R.98, R.100 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:Q.1, E:Q.1, E:V.2 Water bridges: E:R.98 Salt bridges: E:R.98, E:R.100

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

NAG.2: 2 residues within 4Å: Chain A: V.116, N.122 No protein-ligand interaction detected (PLIP) NAG.3: 6 residues within 4Å: Chain A: T.177, Y.179, K.231, N.233, S.235, L.236 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.177, A:K.231, A:N.233 NAG.4: 3 residues within 4Å: Chain A: W.295, R.296, N.297 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.295, A:N.297 Water bridges: A:N.297, A:N.297 NAG.5: 4 residues within 4Å: Chain A: N.345 Chain B: L.264, Q.266, R.332 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.345, B:R.332 Water bridges: A:R.311 NAG.10: 4 residues within 4Å: Chain B: V.116, G.117, N.122, S.125 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.122, B:S.125 NAG.11: 9 residues within 4Å: Chain A: V.217, N.218, W.320 Chain B: T.177, Y.179, K.231, N.233, S.235, L.236 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:V.217, A:N.218, B:T.177, B:K.231, B:N.233 Water bridges: A:Q.306, A:W.320, A:W.320 NAG.12: 4 residues within 4Å: Chain B: Q.294, W.295, R.296, N.297 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.295 Water bridges: B:N.297, B:N.297, B:N.297 NAG.14: 2 residues within 4Å: Chain B: R.311, N.345 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.311 NAG.15: 3 residues within 4Å: Chain B: N.194, S.196, N.197 No protein-ligand interaction detected (PLIP)

3 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.6: 2 residues within 4Å: Chain A: R.74 Chain E: I.28 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:R.74 Hydrophobic interactions: E:I.28 IPA.7: 4 residues within 4Å: Chain A: Y.274, W.320, E.321, G.322 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.274, A:W.320 Water bridges: A:W.320 IPA.13: 7 residues within 4Å: Chain B: S.263, L.264, L.329, I.330, C.381, F.382, L.383 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.264

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

2020-12-30

Peptides

receptor binding protein: AB
Anti-Hendra receptor binding protein antibody HENV-32 Fab heavy chain: CE
Anti-Hendra receptor binding protein antibody HENV-32 Fab light chain: DF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

E
H

D
D

F
L

receptor binding protein

Anti-Hendra receptor binding protein antibody HENV-32 Fab heavy chain

Anti-Hendra receptor binding protein antibody HENV-32 Fab light chain

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