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

Crystal Structure of Fab 32H+109L, a putative precursor of the PGT121 family of potent HIV-1 antibodies

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

hetero-1-1-mer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: Q.37, P.39, A.86, D.87, K.108 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.37, A:D.87 GOL.2: 3 residues within 4Å: Chain A: P.58, R.60, E.81 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.60, A:E.81 Water bridges: A:E.81 GOL.3: 3 residues within 4Å: Chain A: Q.51, D.52, R.53 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.53, A:R.53, A:R.53

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.4: 12 residues within 4Å: Chain A: Q.36, K.38, P.39, Q.41, R.60, F.61, G.83, D.84, K.172, Q.173, S.174, N.176 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.36, A:K.38, A:Q.41, A:D.84, A:D.84 Water bridges: A:R.60, A:K.172

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 8 residues within 4Å: Chain A: V.44, L.45, P.54, S.55, I.57 Chain B: R.97, D.120 Ligands: PG4.6 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.120, A:L.45, A:S.55, A:S.55 Water bridges: B:W.122, A:P.43 PG4.6: 5 residues within 4Å: Chain A: R.53, P.54, S.55, G.56 Ligands: PG4.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.56

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

PGE.7: 3 residues within 4Å: Chain A: Q.200, T.207, E.209 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garces, F. et al., Affinity Maturation of a Potent Family of HIV Antibodies Is Primarily Focused on Accommodating or Avoiding Glycans. Immunity (2015)

Release Date

2015-12-23

Peptides

Antibody 9H+3L Fab light chain: A
Antibody 9H+3L Fab heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Antibody 9H+3L Fab light chain

Antibody 9H+3L Fab heavy chain

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