SMTL ID : 7l8z.1

BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-7 from animal Rh.33311 (Wk26 time point)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-3-3-mer

Ligands

18 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 C: S.365, N.387, S.389 Ligands: NAG.26, NAG.33 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain C: N.297, T.299, H.331, N.333 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain C: Q.295, N.297, N.333 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: N.150, Y.167, L.169, D.322 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.167 NAG-NAG.6: 4 residues within 4Å: Chain C: Q.132, S.152, F.153, N.154 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain C: R.194, N.199, T.200 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain E: E.89, N.90 Chain F: G.8, S.9 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain E: N.387, S.389 Ligands: NAG.40, NAG.47 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain E: N.297, T.299, H.331, N.333, T.415 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain E: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.12 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain E: V.136, N.150, Y.167, L.169, D.322 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.167 NAG-NAG.14: 5 residues within 4Å: Chain C: R.310 Chain E: V.176, R.194, I.196, N.199 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.196 NAG-NAG.15: 4 residues within 4Å: Chain G: N.236, T.238, I.279 Ligands: NAG.51 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain G: N.387, S.389 Ligands: NAG-NAG.22, NAG-NAG.22, NAG.52 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain G: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.18 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain G: Q.132, S.152, F.153, N.154 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain E: R.310 Chain G: R.194, I.196, N.199, T.200 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:I.196 NAG-NAG.22: 7 residues within 4Å: Chain G: N.364, S.365, T.373, N.387, S.389 Ligands: NAG-NAG.16, NAG-NAG.16 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.4: 14 residues within 4Å: Chain C: K.66, P.208, P.214, V.256, L.263, N.264, F.377, N.378, C.379, G.380, I.439, V.446, S.447 Ligands: NAG.28 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.380, C:V.446 NAG-NAG-BMA-MAN-MAN-MAN.18: 12 residues within 4Å: Chain G: E.213, L.263, N.264, F.377, N.378, C.379, G.380, I.439, Q.440, V.446, S.447 Ligands: NAG-NAG.17 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:V.446 Hydrogen bonds: G:G.380, G:V.446

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.12: 10 residues within 4Å: Chain E: S.211, E.213, V.256, L.263, N.264, G.380, R.444, V.446, S.447 Ligands: NAG-NAG.11 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:V.446 Hydrogen bonds: E:G.380, E:V.446

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.19: 4 residues within 4Å: Chain G: N.150, Y.167, L.169, D.322 No protein-ligand interaction detected (PLIP)

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

NAG.23: 5 residues within 4Å: Chain C: N.236, T.238, N.278, I.279 Ligands: NAG.25 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain C: N.243 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain C: E.277, N.278 Ligands: NAG.23 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: N.393 Ligands: NAG-NAG.1 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: N.340, E.341 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain C: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.4 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: N.303, I.324, V.442 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.135 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: E.269, E.270, N.291 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.139 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain C: N.364, S.365, S.366 Ligands: NAG-NAG.1 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain D: N.99, E.102 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain D: E.115, N.118, Y.119 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain D: N.92, T.94 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain E: N.236, T.238, S.276, E.277 Ligands: NAG.39 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain E: D.232, T.242, N.243 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain E: N.278 Ligands: NAG.37 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain E: N.393 Ligands: NAG-NAG.9 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain E: N.340, E.341, W.396 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain E: Q.295, N.297, N.333, R.444 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain E: N.303, I.324, V.442 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain E: Q.132, S.152, F.153, N.154 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain E: N.135, K.149 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain E: N.356 Ligand excluded by PLIP NAG.47: 5 residues within 4Å: Chain E: N.364, S.365, S.366 Ligands: NAG-NAG.9, NAG-NAG.9 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain F: N.118 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain F: N.92, T.94, W.95, I.122 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain G: D.232, T.242, N.243 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain G: N.278 Ligands: NAG-NAG.15 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain G: N.393 Ligands: NAG-NAG.16, NAG-NAG.16 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain G: N.340 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain G: N.297, T.299, H.331, N.333 Ligand excluded by PLIP NAG.55: 5 residues within 4Å: Chain G: Q.295, N.297, N.333, S.335, R.444 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain G: N.303, I.324, V.442 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain G: N.135, T.137 Ligand excluded by PLIP NAG.58: 1 residues within 4Å: Chain G: N.356 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain G: N.291, E.292 Ligand excluded by PLIP NAG.60: 4 residues within 4Å: Chain G: N.138, N.139, I.323, G.325 Ligand excluded by PLIP NAG.61: 2 residues within 4Å: Chain H: N.92, T.94 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Antanasijevic, A. et al., Polyclonal antibody responses to HIV Env immunogens resolved using cryoEM. Nat Commun (2021)

Release Date

2021-08-04

Peptides

Rh.33311 pAbC-7 - Heavy Chain: A
Rh.33311 pAbC-7 - Light Chain: B
BG505 SOSIP.v5.2 N241/N289 - gp120: CEG
BG505 SOSIP.v5.2 N241/N289 - gp41: DFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

E
C

G
D

D
B

F
E

H
F

Rh.33311 pAbC-7 - Heavy Chain

Rh.33311 pAbC-7 - Light Chain

BG505 SOSIP.v5.2 N241/N289 - gp120

BG505 SOSIP.v5.2 N241/N289 - gp41

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