SMTL ID : 7l8y.1

BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-5 from animal Rh.33311 (Wk26 time point)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-3-3-mer

Ligands

10 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: 2 residues within 4Å: Chain C: G.390, N.393 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain C: N.364, S.365, T.373, N.387, T.388, S.389 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain C: V.136, N.138, N.150, Y.167, L.169, D.322 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.167 NAG-NAG.5: 4 residues within 4Å: Chain C: Q.132, S.152, F.153, N.154 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain E: T.374, N.387, S.389 Ligands: NAG.31 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain E: N.297, T.299, H.331, N.333 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 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.10: 4 residues within 4Å: Chain G: S.365, T.373, N.387, S.389 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 7 residues within 4Å: Chain G: N.297, C.298, T.299, R.328, H.331, N.333, T.415 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.328 NAG-NAG.13: 5 residues within 4Å: Chain G: N.138, N.150, Y.167, L.169, D.322 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Y.167

3 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.3: 8 residues within 4Å: Chain C: S.211, E.213, V.256, L.263, N.264, V.446, S.447 Ligands: NAG.19 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.446 Hydrogen bonds: C:V.446 NAG-NAG-BMA-MAN-MAN.8: 11 residues within 4Å: Chain E: H.68, E.213, P.214, V.256, L.263, N.264, C.379, G.380, V.446, S.447 Ligands: NAG.33 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.380, E:V.446 NAG-NAG-BMA-MAN-MAN.12: 10 residues within 4Å: Chain G: S.211, E.213, P.214, V.256, L.263, N.264, G.380, V.446, S.447 Ligands: NAG.51 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:G.380, G:V.446

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

NAG.14: 5 residues within 4Å: Chain C: W.98, N.236, G.237, T.238, S.276 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain C: T.242, N.243 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain C: N.340, E.341, W.396 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain C: N.297, T.299, H.331, N.333 Ligand excluded by PLIP NAG.18: 6 residues within 4Å: Chain C: Q.295, N.297, N.333, V.334, S.335, R.444 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain C: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.3 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain C: N.303, I.324, V.442 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain C: R.194, N.199, T.200 Chain G: R.310 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain C: N.135, K.149 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain C: N.291, E.292, K.345 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain C: N.139 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain D: N.118, Y.119 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain D: N.92, T.94 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain E: E.89, N.90 Chain F: S.9 Ligand excluded by PLIP NAG.28: 6 residues within 4Å: Chain E: K.234, F.235, N.236, G.237, T.238, I.279 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain E: T.242, N.243 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain E: N.278, T.280, N.281 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain E: N.393 Ligands: NAG-NAG.6 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain E: Q.295, N.297, N.333 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain E: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.8 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain E: N.303, I.324, V.442 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain E: Q.132, S.152, F.153, N.154 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: R.310 Chain E: R.194, N.199, T.200 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain E: N.135, Q.177, Y.193 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain E: R.351, G.355, N.356 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain E: E.270, N.291, E.292, K.348 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain A: X.93 Chain B: X.47 Chain E: N.462 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain E: K.336, N.340 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain F: N.118, Y.119 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain F: N.92, T.94 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain G: E.89, N.90 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain G: N.236, T.238, G.239, S.276, I.279 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain G: N.243 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain G: N.278, T.280 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain G: S.389, N.393 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain G: N.340, E.341, W.396 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain G: Q.295, N.297, N.333 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain G: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.12 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain G: N.303, I.324, V.442 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain G: Q.132, S.152, F.153, N.154 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain E: R.310 Chain G: R.194, N.199, T.200 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain G: N.135, K.149 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain G: N.356 Ligand excluded by PLIP NAG.57: 5 residues within 4Å: Chain G: E.270, E.271, V.272, N.291, E.292 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain H: N.92, T.94, W.95, Y.119 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-5 - Heavy Chain: A
Rh.33311 pAbC-5 - 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
C

E
A

G
E

D
D

F
B

H
F

Rh.33311 pAbC-5 - Heavy Chain

Rh.33311 pAbC-5 - Light Chain

BG505 SOSIP.v5.2 N241/N289 - gp120

BG505 SOSIP.v5.2 N241/N289 - gp41

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