SMTL ID : 7l8u.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

9 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: 3 residues within 4Å: Chain A: T.374, N.387, S.389 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 8 residues within 4Å: Chain A: E.213, L.263, N.264, F.377, R.444, C.445, V.446, S.447 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.446 NAG-NAG.3: 6 residues within 4Å: Chain A: V.136, N.138, N.150, Y.167, L.169, D.322 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.167 NAG-NAG.4: 4 residues within 4Å: Chain C: S.365, T.373, N.387, S.389 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain C: V.136, N.150, Y.167, L.169, D.322 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.167 NAG-NAG.7: 4 residues within 4Å: Chain D: N.99, S.101, E.102 Chain G: X.54 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain E: E.89, N.90 Chain F: G.5, G.8, S.9 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain E: N.364, T.373, N.387, S.389 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 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

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.5: 11 residues within 4Å: Chain C: K.209, P.214, V.256, L.263, N.264, C.379, G.380, C.445, V.446, S.447 Ligands: NAG.36 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.446 Hydrogen bonds: C:G.380, C:V.446, C:K.209

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN.8: 3 residues within 4Å: Chain D: N.92 Chain G: X.96, X.97 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.11: 9 residues within 4Å: Chain E: S.211, P.214, L.263, N.264, F.377, C.379, V.446, S.447 Ligands: NAG.51 No protein-ligand interaction detected (PLIP)

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

NAG.13: 1 residues within 4Å: Chain A: N.90 Ligand excluded by PLIP NAG.14: 6 residues within 4Å: Chain A: N.236, T.238, S.276, E.277, N.278, I.279 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: T.242, N.243 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.278, N.281 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: G.390, N.393 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: A.337, N.340, E.341 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: N.297, T.299, H.331, N.333 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: Q.295, N.297, N.333, R.444 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: S.293, V.446, S.447, N.448 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: N.303, I.324, V.442 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: S.152, F.153, N.154 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: R.194, N.199, T.200 Chain E: R.310 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.135, K.149 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.356 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain A: E.269, E.271, N.291, E.292, K.345 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain C: E.89, N.90 Chain D: G.8, S.9 Ligand excluded by PLIP NAG.29: 6 residues within 4Å: Chain C: N.236, S.276, E.277, N.278, I.279 Ligands: NAG.31 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: K.231, K.233, N.243 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain C: N.278, T.280, N.281 Ligands: NAG.29 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: G.390, N.393 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain C: N.340, S.394, T.395, W.396 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain C: N.297, T.299, H.331, N.333 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: Q.295, N.297, N.333, R.444 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.5 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.303, V.442 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: S.152, F.153, N.154 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain A: R.310 Chain C: R.194, N.199, T.200 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.135, G.146 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.356 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain C: E.270, N.291, E.292, K.345 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain D: K.114, E.115, S.117, N.118, Y.119 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain D: E.102, N.106 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain E: N.236, T.238, G.239 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain E: N.243 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain E: N.278, T.280, N.281 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain E: S.389, G.390, N.393 Ligand excluded by PLIP NAG.49: 5 residues within 4Å: Chain E: N.297, T.299, H.331, N.333, R.444 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain E: Q.295, N.297, N.333 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain E: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.11 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain E: N.303, I.324, V.442 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain E: Q.132, F.153, N.154, K.165 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain C: R.310 Chain E: N.199 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain E: N.135, K.149 Ligand excluded by PLIP NAG.56: 6 residues within 4Å: Chain E: E.269, E.270, E.271, N.291, E.292, K.345 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain F: N.99, S.101, E.102 Ligand excluded by PLIP NAG.58: 1 residues within 4Å: Chain F: N.118 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain F: 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

BG505 SOSIP.v5.2 N241/N289 - gp120: ACE
BG505 SOSIP.v5.2 N241/N289 - gp41: BDF
Rh.33311 pAbC-2 - Heavy Chain: G
Rh.33311 pAbC-2 - Light Chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
A

E
E

B
D

D
B

F
F

G
H

H
L

BG505 SOSIP.v5.2 N241/N289 - gp120

BG505 SOSIP.v5.2 N241/N289 - gp41

Rh.33311 pAbC-2 - Heavy Chain

Rh.33311 pAbC-2 - Light Chain

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