SMTL ID : 5nuz.1 (1 other biounit)

Junin virus GP1 glycoprotein in complex with an antibody Fab fragment

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-1-1-1-mer

Ligands

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.1: 8 residues within 4Å: Chain C: N.95, S.97, T.99, G.100, V.101, N.102, L.129, L.131 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.99

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: K.41, E.49, K.66, F.67, E.92 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.41, A:K.41 Water bridges: A:E.49 GOL.3: 4 residues within 4Å: Chain A: K.22, T.74, V.76, Y.83 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.22, A:K.22, A:T.74 GOL.4: 4 residues within 4Å: Chain A: S.130, V.131, K.218 Chain B: E.130 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.131, A:K.218, B:E.130 GOL.7: 7 residues within 4Å: Chain A: D.108 Chain B: D.34, F.39, S.98, K.99 Chain C: D.30, I.32 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:D.108, B:D.34, B:D.34, B:K.99 Water bridges: A:R.102, B:Y.103 GOL.8: 9 residues within 4Å: Chain A: F.176, V.179, T.186, L.187, S.188 Chain B: L.167, S.169, S.183, T.185 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:L.167, B:S.183, B:T.185, A:S.188, A:S.188 GOL.9: 6 residues within 4Å: Chain A: N.103, Y.109 Chain B: L.53, Y.56, G.62, S.63 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.63 Water bridges: B:S.63, A:D.111 GOL.11: 1 residues within 4Å: Chain C: N.126 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.126 Water bridges: C:N.126

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

IPA.5: 4 residues within 4Å: Chain A: Y.63, K.68, G.69, A.71 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.67, A:G.69 IPA.6: 4 residues within 4Å: Chain A: V.96, Q.115, G.116, T.118 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.96 Hydrogen bonds: A:Q.115

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

NAG.10: 4 residues within 4Å: Chain C: V.41, W.51, N.83, T.85 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.41, C:W.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeltina, A. et al., Convergent immunological solutions to Argentine hemorrhagic fever virus neutralization. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-06-28

Peptides

eOD01 heavy chain: A
eOD01 light chain: B
Pre-glycoprotein polyprotein GP complex: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

eOD01 heavy chain

eOD01 light chain

Pre-glycoprotein polyprotein GP complex

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