SMTL ID : 5i9q.1 (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- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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.1: 10 residues within 4Å: Chain A: E.19, E.21, T.93, D.95, P.96, K.136, N.146, N.244, K.299, S.300 No protein-ligand interaction detected (PLIP)

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

NAG.2: 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:N.118, A:N.118, A:N.124 NAG.3: 5 residues within 4Å: Chain A: V.42, L.43, E.44, N.113, N.125 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.42 NAG.4: 2 residues within 4Å: Chain A: S.202, N.205 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.202 NAG.5: 2 residues within 4Å: Chain A: N.253, S.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.253, A:S.255 NAG.6: 2 residues within 4Å: Chain A: I.262, N.264 No protein-ligand interaction detected (PLIP) NAG.9: 4 residues within 4Å: Chain C: T.20, T.22, W.64, N.69 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.64

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

EDO.7: 6 residues within 4Å: Chain A: V.139, E.237, S.242, F.243, W.280, M.328 No protein-ligand interaction detected (PLIP) EDO.8: 1 residues within 4Å: Chain A: K.285 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

426c.TM4dV1-3 p120: A
3BNC55 Fab heavy chain: B
3BNC55 light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

426c.TM4dV1-3 p120

3BNC55 Fab heavy chain

3BNC55 light chain

Related Entries With Identical Sequence