SMTL ID : 7l90.1

BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-8 from animal Rh.33311 (Wk26 time point)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

7 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 A: N.364, T.373, N.387, S.389 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: V.136, N.150, Y.167, L.169, D.322 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.167 NAG-NAG.4: 2 residues within 4Å: Chain B: N.92, T.94 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain C: N.364, T.373, N.387, T.388, S.389 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 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.8: 5 residues within 4Å: Chain E: S.365, T.373, T.374, N.387, S.389 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.365, E:S.365 NAG-NAG.10: 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

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.2: 7 residues within 4Å: Chain A: E.213, V.256, L.263, N.264, V.446, S.447 Ligands: NAG.14 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.446 Hydrogen bonds: A:V.446 NAG-NAG-BMA-MAN.6: 9 residues within 4Å: Chain C: E.213, V.256, L.263, N.264, G.380, C.445, V.446, S.447 Ligands: NAG.36 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.446 Hydrogen bonds: C:G.380, C:V.446 NAG-NAG-BMA-MAN.9: 11 residues within 4Å: Chain E: E.213, P.214, V.256, L.263, N.264, G.380, R.444, C.445, V.446, S.447 Ligands: NAG.54 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:V.446 Hydrogen bonds: E:G.380, E:V.446

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

NAG.11: 3 residues within 4Å: Chain A: S.389, G.390, N.393 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: N.340, E.341, T.395, W.396 Ligand excluded by PLIP NAG.13: 5 residues within 4Å: Chain A: N.297, T.299, H.331, N.333, R.444 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: V.446, S.447, N.448 Ligands: NAG-NAG-BMA-MAN.2 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.135, G.146, K.149 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.139, I.140, D.326 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: Q.132, S.152, F.153, N.154 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: N.199, T.200 Chain E: R.310, W.316 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: N.236, G.237, T.238, S.276 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.90 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain A: E.269, E.270, N.291, E.292, K.345 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.356 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: K.233, T.242, N.243 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: N.278, T.280, N.281 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.303, I.324, V.442 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: Q.295, N.297, N.333 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: S.117, N.118 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.99, E.102 Ligand excluded by PLIP NAG.29: 7 residues within 4Å: Chain C: N.236, T.238, S.276, E.277, N.278, I.279 Ligands: NAG.31 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: D.232, T.242, N.243 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain C: N.278, I.279, T.280 Ligands: NAG.29 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: S.389, G.390, N.393 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: N.340, E.341, 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, S.335 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: V.446, S.447, N.448 Ligands: NAG-NAG-BMA-MAN.6 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.303, I.324, V.442 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain C: Q.132, S.152, F.153, N.154, K.165 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, K.149 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.356 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain C: E.270, E.271, N.291, K.345, Q.349 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: E.89, N.90 Chain D: T.10 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain D: N.92, T.94, W.95, Y.119 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain D: N.118 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain E: E.89, N.90 Chain F: G.8, S.9 Ligand excluded by PLIP NAG.47: 7 residues within 4Å: Chain E: N.236, T.238, G.239, P.240, S.276, E.277, I.279 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain E: D.232, N.243 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain E: N.278, I.279, T.280 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain E: G.390, N.393 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain E: N.340, W.396 Ligand excluded by PLIP NAG.52: 5 residues within 4Å: Chain E: N.297, T.299, H.331, N.333, T.415 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain E: Q.295, N.297, N.333, R.444 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain E: N.264, N.448 Ligands: NAG-NAG-BMA-MAN.9 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain E: N.303, I.324, V.442 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain E: Q.132, S.152, F.153, N.154 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain C: R.310 Chain E: R.194, N.199, T.200 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain E: T.134, N.135, T.137 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain E: G.355, N.356 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain E: E.270, E.271, N.291 Ligand excluded by PLIP NAG.61: 3 residues within 4Å: Chain F: N.99, S.101, E.102 Ligand excluded by PLIP NAG.62: 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-8 - Heavy Chain: G
Rh.33311 pAbC-8 - Light Chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
H

H
L

BG505 SOSIP.v5.2 N241/N289 - gp120

BG505 SOSIP.v5.2 N241/N289 - gp41

Rh.33311 pAbC-8 - Heavy Chain

Rh.33311 pAbC-8 - Light Chain

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