SMTL ID : 5i9q.2 (1 other biounit)

Crystal structure of 3BNC55 Fab in complex with 426c.TM4deltaV1-3 gp120

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-1-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: 10 residues within 4Å: Chain A: T.93, D.95, K.136, L.145, N.146, F.243, T.297, C.298, K.299, S.300 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.297

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

NAG.2: 4 residues within 4Å: Chain A: L.236, T.240, N.253, S.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.253, A:S.255 NAG.3: 5 residues within 4Å: Chain A: N.114, T.116, F.117, N.118, N.124 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.116, A:N.118, A:N.124 NAG.4: 3 residues within 4Å: Chain A: V.42, N.113, N.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.125 NAG.7: 4 residues within 4Å: Chain C: T.20, T.22, R.62, N.69 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:R.62 Hydrogen bonds: C:R.62, C:N.69

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 4 residues within 4Å: Chain A: N.81 Chain B: T.28, T.30, E.77 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.81, B:T.30, B:E.77

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 1 residues within 4Å: Chain A: K.274 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.274

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.TM4dV1-3 p120: A
3BNC55 Fab heavy chain: B
3BNC55 light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

426c.TM4dV1-3 p120

3BNC55 Fab heavy chain

3BNC55 light chain

Related Entries With Identical Sequence