SMTL ID : 7mdu.1

BG505 SOSIP MD39 in complex with the monoclonal antibodies Rh.33104 mAb.1 and RM20A3

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

8 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain B: N.138, N.150, Y.167, D.322 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain B: R.194, N.199 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain B: N.236, G.237, T.238, P.240, S.276, H.353 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.240 NAG-NAG.5: 3 residues within 4Å: Chain B: N.278, T.280, N.281 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain B: Q.295, N.297, N.333, V.334, S.335, R.444 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.297, T.299, H.331, N.333 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain B: Q.364, T.373, T.374, N.387, S.389 Ligands: NAG.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.364 NAG-NAG.9: 3 residues within 4Å: Chain B: E.89, N.90 Chain F: S.17 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: 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.4: 9 residues within 4Å: Chain B: E.213, V.256, L.263, N.264, N.378, G.380, V.446, S.447 Ligands: NAG.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.446

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

NAG.10: 1 residues within 4Å: Chain B: N.135 No protein-ligand interaction detected (PLIP) NAG.11: 3 residues within 4Å: Chain B: S.152, F.153, N.154 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain B: N.303, I.324, V.442 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.442 Hydrogen bonds: B:N.303 NAG.13: 2 residues within 4Å: Chain B: N.340, T.400 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.340, B:T.400 NAG.14: 3 residues within 4Å: Chain B: S.389, N.393 Ligands: NAG-NAG.8 No protein-ligand interaction detected (PLIP) NAG.15: 4 residues within 4Å: Chain B: N.264, P.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.4 No protein-ligand interaction detected (PLIP) NAG.16: 3 residues within 4Å: Chain B: N.139, I.324, G.325 No protein-ligand interaction detected (PLIP) NAG.17: 1 residues within 4Å: Chain B: N.356 No protein-ligand interaction detected (PLIP) NAG.18: 3 residues within 4Å: Chain B: S.398, N.399 Chain E: S.60 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:V.58, E:S.60, E:S.60 NAG.19: 2 residues within 4Å: Chain F: N.100, S.102 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.102 NAG.20: 3 residues within 4Å: Chain F: E.123, N.126, Y.127 No protein-ligand interaction detected (PLIP) NAG.21: 2 residues within 4Å: Chain F: N.107, S.109 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Antanasijevic, A. et al., From structure to sequence: Antibody discovery using cryoEM. Sci Adv (2022)

Release Date

2022-01-26

Peptides

Rh.33104 mAb.1 Heavy Chain: A
Surface protein gp120: B
RM20A3 mAb Heavy Chain: C
RM20A3 mAb Light Chain: D
Rh.33104 mAb.1 Light Chain: E
Transmembrane protein gp41: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
A

C
E

D
F

E
L

F
B

Rh.33104 mAb.1 Heavy Chain

Surface protein gp120

RM20A3 mAb Heavy Chain

RM20A3 mAb Light Chain

Rh.33104 mAb.1 Light Chain

Transmembrane protein gp41

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