SMTL ID : 6uum.1 (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

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

PG4.1: 8 residues within 4Å: Chain A: Q.39, R.40, R.41, V.86, P.101, G.102, Q.104 Ligands: PG4.2 No protein-ligand interaction detected (PLIP) PG4.2: 8 residues within 4Å: Chain A: Q.39, V.86, S.88 Chain B: Q.39, Q.43, G.44, L.45 Ligands: PG4.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.39 PG4.4: 7 residues within 4Å: Chain A: W.33, G.94, S.95 Chain B: I.57, Y.58, Y.113, N.114 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:W.33, A:G.94, B:Y.58 PG4.13: 4 residues within 4Å: Chain A: Q.161 Chain B: S.88, S.189 Ligands: PG4.14 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:S.189, A:G.158 PG4.14: 8 residues within 4Å: Chain B: S.88, V.128, L.187, Q.188, S.189, G.191 Ligands: PG4.13, PG4.16 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.88 PG4.15: 4 residues within 4Å: Chain B: V.93, Y.95, P.122 Ligands: PG4.16 1 PLIP interactions: 1 interactions with chain B Water bridges: B:V.93 PG4.16: 14 residues within 4Å: Chain A: Q.161 Chain B: P.41, T.91, G.92, V.93, K.125, I.127, E.165, A.185, V.186, L.187, Y.193 Ligands: PG4.14, PG4.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.187 Water bridges: B:V.93

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

NAG.3: 3 residues within 4Å: Chain A: S.26, Q.27, N.28 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.28, A:N.28

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

SO4.5: 4 residues within 4Å: Chain A: R.55, F.63, T.64, R.66 6 PLIP interactions: 6 interactions with chain A Water bridges: A:S.53, A:R.66, A:R.66, A:R.66 Salt bridges: A:R.55, A:R.66 SO4.6: 1 residues within 4Å: Chain A: D.61 No protein-ligand interaction detected (PLIP) SO4.7: 3 residues within 4Å: Chain A: R.66, G.67, S.68 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.67 SO4.8: 5 residues within 4Å: Chain A: R.40, R.46, P.60, R.62, E.82 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.82, A:E.82 Water bridges: A:R.40, A:R.46, A:R.62, A:R.62 Salt bridges: A:R.40, A:R.46, A:R.62 SO4.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.10: 3 residues within 4Å: Chain A: S.157, G.158, S.160 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.158 Water bridges: A:Q.156, A:S.160, A:S.160 SO4.11: 4 residues within 4Å: Chain A: S.122, D.123, E.124 Chain B: P.140 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:K.231 Hydrogen bonds: A:S.122, A:D.123, A:E.124 SO4.17: 6 residues within 4Å: Chain B: V.2, G.27, T.28, F.32, R.98, G.101 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.28, B:T.28 Salt bridges: B:R.98 SO4.18: 3 residues within 4Å: Chain A: F.96 Chain B: K.59, H.65 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Y.60 Salt bridges: B:K.59, B:H.65 SO4.19: 4 residues within 4Å: Chain B: T.28, F.29, T.30, K.77 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.29, B:T.30

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

ACT.12: 0 residues within 4Å: (No contacts) 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
F

B
H

B11 Fab Light Chain

B11 DSS Fab Heavy Chain

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