SMTL ID : 6uum.2 (1 other biounit)

Crystal structure of antibody 438-B11 DSS mutant (Cys98A-Cys100aA)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

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

PG4.1: 1 residues within 4Å: Chain A: T.64 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.66 PG4.2: 6 residues within 4Å: Chain A: R.41, V.86, G.102, Q.104 Chain B: G.42 Ligands: PG4.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.40 PG4.3: 3 residues within 4Å: Chain A: Q.104, R.143 Ligands: PG4.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.104 PG4.5: 5 residues within 4Å: Chain B: P.14, G.15, S.85 Ligands: PG4.6, ACT.12 No protein-ligand interaction detected (PLIP) PG4.6: 10 residues within 4Å: Chain B: P.14, T.87, S.88, V.128, L.187, Q.188, S.189, G.191 Ligands: PG4.5, ACT.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.88 PG4.7: 8 residues within 4Å: Chain A: Q.161 Chain B: P.41, I.127, E.165, A.185, V.186, L.187, Y.193 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.127, B:Y.193 Hydrogen bonds: B:L.187, A:Q.161

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

NAG.4: 3 residues within 4Å: Chain A: S.26, N.28, T.70 No protein-ligand interaction detected (PLIP)

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 4 residues within 4Å: Chain B: T.28, F.29, T.30, K.77 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.29, B:T.30, B:T.30 Salt bridges: B:K.77 SO4.9: 6 residues within 4Å: Chain B: V.2, G.27, T.28, F.32, R.98, G.101 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.28, B:T.28 Water bridges: B:G.26 Salt bridges: B:R.98 SO4.10: 3 residues within 4Å: Chain B: V.93, P.122, G.123 No protein-ligand interaction detected (PLIP) SO4.11: 4 residues within 4Å: Chain A: Q.161, T.181 Chain B: Q.188, S.189 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.188, B:S.189, A:T.181 Water bridges: A:T.181, A:T.181

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.12: 2 residues within 4Å: Ligands: PG4.5, PG4.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, S. et al., A V H 1-69 antibody lineage from an infected Chinese donor potently neutralizes HIV-1 by targeting the V3 glycan supersite. Sci Adv (2020)

Release Date

2020-09-23

Peptides

B11 Fab Light Chain: A
B11 DSS Fab Heavy Chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

B11 Fab Light Chain

B11 DSS Fab Heavy Chain

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