SMTL ID : 7syy.1

Hendra virus G protein head domain in complex with cross-neutralizing murine antibody hAH1.3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.74 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- FUC- FUC: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC-FUC.1: 9 residues within 4Å: Chain A: R.495, F.496, N.497, N.529 Chain B: Y.102, D.103, G.104 Chain C: N.35, K.55 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: A:N.497 Hydrogen bonds: C:N.35, C:K.55, B:G.104

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.2: 10 residues within 4Å: Chain A: D.433, N.434, R.476, Q.478, W.479, R.480, N.481 Chain C: D.1, Q.27, H.98 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.1, C:D.1, C:Q.27 Water bridges: C:V.99, A:N.434

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: 7 residues within 4Å: Chain A: T.361, Y.363, K.415, N.417, S.419, L.420 Ligands: CL.10 No protein-ligand interaction detected (PLIP)

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.4: 6 residues within 4Å: Chain A: Q.376, Y.377, N.378, N.381 Chain B: D.62, K.65 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.65, A:N.381 Water bridges: A:N.378

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

NAG.5: 3 residues within 4Å: Chain A: V.300, N.306, S.309 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.309

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

SO4.6: 7 residues within 4Å: Chain A: H.386, C.387, K.388, Y.389 Chain B: Y.101, Y.102, D.103 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.102, B:D.103, A:K.388, A:Y.389 SO4.7: 7 residues within 4Å: Chain A: S.307, T.308, V.401, N.402, S.405, H.406, Y.407 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.307, A:S.307, A:T.308, A:N.402, A:H.406, A:Y.407, A:Y.407 Water bridges: A:S.405 SO4.8: 6 residues within 4Å: Chain A: K.344, L.370, E.374, F.375, Q.376, R.410 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.376, A:Q.376, A:R.410 Salt bridges: A:K.344 SO4.15: 7 residues within 4Å: Chain B: V.160, T.161, W.162, G.165, L.167, S.168, V.171 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.162, B:G.165, B:G.165 SO4.16: 4 residues within 4Å: Chain B: S.128, K.151, G.152, Q.179 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.128, B:Q.179 SO4.17: 3 residues within 4Å: Chain B: K.38, K.46, F.64 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.38, B:K.46

1 x ZN: ZINC ION(Non-covalent)

ZN.9: 3 residues within 4Å: Chain A: K.344, D.346, E.374 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.346

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

CL.10: 3 residues within 4Å: Chain A: D.360, T.361 Ligands: NAG-NAG.3 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: R.372, R.396 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: V.182, G.183, L.448, G.449 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: R.201, W.573, K.596 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: H.299, V.300, W.310, T.311 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: T.28, N.31, Y.32 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: A.61, D.62 Chain C: P.100 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain B: K.106, A.107 Chain C: K.55 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain B: A.122, K.123, L.182 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain C: R.160, H.194 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Z. et al., Potent monoclonal antibody-mediated neutralization of a divergent Hendra virus variant. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-06-01

Peptides

Attachment glycoprotein: A
Antibody hAH1.3 Heavy Chain: B
Antibody hAH1.3 light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Attachment glycoprotein

Antibody hAH1.3 Heavy Chain

Antibody hAH1.3 light chain

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