SMTL ID : 5fec.2 (1 other biounit)

Crystal structure of 3BNC60 Fab germline precursor in complex with 426c.TM4deltaV1-3 gp120

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.17 Å

Oligo State

hetero-1-1-2-mer

Ligands

1 x NAG- NAG- BMA- MAN: 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.1: 5 residues within 4Å: Chain C: T.93, K.136, N.146, K.299, S.300 No protein-ligand interaction detected (PLIP)

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

NAG.2: 4 residues within 4Å: Chain C: T.239, T.240, N.253, S.255 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.240 Hydrogen bonds: C:N.253, C:S.255 NAG.3: 6 residues within 4Å: Chain C: E.152, E.153, I.154, N.173, Q.212, K.215 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:I.154, C:N.173, C:Q.212, C:K.215 NAG.4: 3 residues within 4Å: Chain C: V.42, N.113, N.125 No protein-ligand interaction detected (PLIP) NAG.5: 5 residues within 4Å: Chain C: G.256, N.259, T.261, I.262, S.263 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.259, C:S.263 NAG.7: 3 residues within 4Å: Chain D: T.240, N.253, S.255 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.255 NAG.8: 5 residues within 4Å: Chain D: E.152, E.153, I.154, N.173, Q.212 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.154 Hydrogen bonds: D:I.154, D:N.173 NAG.9: 6 residues within 4Å: Chain D: G.256, N.259, T.261, I.262, S.263, I.267 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.259, D:S.263 NAG.10: 2 residues within 4Å: Chain D: I.262, N.264 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:I.262

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.6: 9 residues within 4Å: Chain D: E.19, T.93, D.95, P.96, K.136, V.138, N.146, N.244, K.299 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scharf, L. et al., Structural basis for germline antibody recognition of HIV-1 immunogens. Elife (2016)

Release Date

2016-05-04

Peptides

germline 3BNC60 heavy chain: A
germline 3BNC60 light chain: B
426c.TM4deltaV1-3 gp120: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
C

germline 3BNC60 heavy chain

germline 3BNC60 light chain

426c.TM4deltaV1-3 gp120

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