SMTL ID : 7mdt.1

BG505 SOSIP.v5.2 in complex with the monoclonal antibody Rh4O9.8 (as Fab fragment)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

16 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: 5 residues within 4Å: Chain A: V.136, N.138, N.150, Y.167, D.322 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.167 NAG-NAG.2: 6 residues within 4Å: Chain A: N.138, N.139, G.325 Chain C: Y.50, S.57 Chain D: Y.103 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.50 NAG-NAG.4: 7 residues within 4Å: Chain A: N.297, C.298, T.299, H.331, N.333, R.444 Chain D: T.28 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 7 residues within 4Å: Chain A: V.176, R.194, L.195, I.196, N.197, C.198, N.199 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.387, S.389 Ligands: NAG.21, NAG.30 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: Q.132, N.154, K.163 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 7 residues within 4Å: Chain A: N.264, L.267, P.293, V.446, S.447, N.448 Ligands: NAG-NAG-BMA-MAN.8 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain E: V.136, N.138, N.150, S.152, Y.167, D.322 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.167 NAG-NAG.11: 5 residues within 4Å: Chain E: N.297, T.299, H.331, N.333, R.444 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain E: N.387, S.389 Ligands: NAG.33, NAG.34 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain E: Q.132, N.154, K.163 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain F: V.136, N.138, N.150, Y.167, D.322 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain F: N.297, T.299, H.331, N.333 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 7 residues within 4Å: Chain F: V.176, R.194, L.195, I.196, N.197, C.198, N.199 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain F: T.373, T.374, N.387, S.389 Ligands: NAG.45 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain F: N.264, P.293, N.448 Ligands: NAG-NAG-BMA-MAN.19 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 6 residues within 4Å: Chain A: N.135, R.145 Chain C: D.94, N.95, S.97 Chain D: Y.59 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.97, C:S.97

3 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.8: 10 residues within 4Å: Chain A: E.213, V.256, L.263, N.264, F.377, C.379, G.380, V.446, S.447 Ligands: NAG-NAG.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.380 NAG-NAG-BMA-MAN.14: 8 residues within 4Å: Chain E: E.213, L.263, N.264, F.377, N.378, C.379, V.446 Ligands: NAG.41 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:V.446 NAG-NAG-BMA-MAN.19: 8 residues within 4Å: Chain F: E.213, L.263, N.264, C.379, G.380, V.446, S.447 Ligands: NAG-NAG.20 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:G.380

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

NAG.21: 3 residues within 4Å: Chain A: N.393 Ligands: NAG-NAG.6, NAG-NAG.6 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: E.89, N.90 Chain B: G.16, S.17 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: N.236, T.238, S.276, I.279 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.278, N.281 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain A: Q.295, N.297, N.333, S.335 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.356 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: T.461, N.462 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: N.303, I.324, V.442 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain A: N.340 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain A: N.364, S.365, T.373 Ligands: NAG-NAG.6, NAG-NAG.6 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain E: N.139, I.323, I.324, G.325 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain E: C.133, N.135 Ligand excluded by PLIP NAG.33: 6 residues within 4Å: Chain E: N.364, S.365, G.367, T.373 Ligands: NAG-NAG.12, NAG-NAG.12 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain E: N.393 Ligands: NAG-NAG.12, NAG-NAG.12 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain E: E.89, N.90 Chain G: G.16, S.17 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain E: N.236, I.279 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain E: N.278, T.280, N.281 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain E: Q.295, N.297, N.333, S.335 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain E: N.356 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain E: N.303, I.324, V.442 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain E: P.293, V.446, N.448 Ligands: NAG-NAG-BMA-MAN.14 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain E: N.340, W.396 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain F: N.139, I.323, I.324, G.325 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain F: C.133, T.134, N.135, K.191 Ligand excluded by PLIP NAG.45: 6 residues within 4Å: Chain F: N.364, S.365, G.367, T.373 Ligands: NAG-NAG.18, NAG-NAG.18 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain F: E.89, N.90 Chain H: G.16, S.17 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain F: N.236, T.238, S.276, I.279 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain F: N.278 Ligand excluded by PLIP NAG.49: 5 residues within 4Å: Chain F: Q.295, N.297, N.333, S.335, R.444 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain F: N.303, I.324 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain F: Q.132, N.154 Ligand excluded by PLIP

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

Surface protein gp120: AEF
Transmembrane protein gp41: BGH
Rh4O9.8 monoclonal antibody Light Chain: C
Rh4O9.8 monoclonal antibody Heavy Chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
C

F
E

B
B

G
D

H
F

C
L

D
H

Surface protein gp120

Transmembrane protein gp41

Rh4O9.8 monoclonal antibody Light Chain

Rh4O9.8 monoclonal antibody Heavy Chain

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