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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.17 Å

Oligo State

hetero-2-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]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-MAN-MAN.1: 10 residues within 4Å: Chain A: E.19, T.93, D.95, P.96, K.136, V.138, N.146, C.298, K.299, S.300 No protein-ligand interaction detected (PLIP)

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.2: 8 residues within 4Å: Chain B: K.136, L.145, N.146, C.245, T.297, C.298, K.299, S.300 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.297

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

NAG.3: 6 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, Q.212, K.216 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.154, A:N.173 NAG.4: 3 residues within 4Å: Chain A: T.240, N.253, S.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.253, A:S.255 NAG.5: 6 residues within 4Å: Chain A: G.256, N.259, T.261, I.262, S.263, I.267 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.267 Hydrogen bonds: A:N.259, A:S.263 NAG.6: 1 residues within 4Å: Chain A: N.264 No protein-ligand interaction detected (PLIP) NAG.7: 4 residues within 4Å: Chain A: A.88 Chain B: T.240, N.253, S.255 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.88 Hydrogen bonds: B:S.255 NAG.8: 6 residues within 4Å: Chain B: G.256, N.259, T.261, I.262, S.263, I.267 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:S.263, B:I.267 Hydrogen bonds: B:N.259, B:S.263 NAG.9: 6 residues within 4Å: Chain B: E.152, E.153, I.154, N.173, Q.212, K.216 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.153, B:I.154, B:N.173

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

426c.TM4deltaV1-3 gp120: AB
germline 3BNC60 heavy chain: C
germline 3BNC60 light chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
I

C
H

D
L

426c.TM4deltaV1-3 gp120

germline 3BNC60 heavy chain

germline 3BNC60 light chain

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