SMTL ID : 7l8x.1

BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-4 from animal Rh.33311 (Wk26 time point)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

20 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: S.389, G.390, N.393 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: T.374, N.387, S.389 Ligands: NAG.37 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: N.297, T.299, H.331, N.333, R.444 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: V.136, N.138, N.150, Y.167, L.169 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.167 NAG-NAG.6: 2 residues within 4Å: Chain B: N.92, T.94 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain C: E.89, N.90 Chain D: G.5, G.8, S.9 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.393 Ligands: NAG-NAG.9, NAG.51 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain C: N.387, S.389, R.419 Ligands: NAG-NAG.8, NAG.51 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: N.297, H.331, N.333, T.415 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: Q.295, N.297, N.333, S.335 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 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.14: 2 residues within 4Å: Chain D: N.92, T.94 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain G: E.89, N.90 Chain H: G.8, S.9 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain G: S.389, G.390, N.393 Ligands: NAG-NAG.17 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 6 residues within 4Å: Chain G: N.387, S.389, R.419 Ligands: NAG-NAG.16, NAG-NAG.22, NAG-NAG.22 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain G: N.297, T.299, H.331, N.333 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain G: Q.295, N.297, N.333, R.444 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain E: X.54 Chain G: I.178, R.194, N.199, T.200 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:I.178 Hydrogen bonds: G:N.179 NAG-NAG.22: 7 residues within 4Å: Chain G: N.364, S.365, T.373, N.387, S.389 Ligands: NAG-NAG.17, NAG-NAG.17 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain H: N.92, T.94, W.95 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- BMA- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-BMA-MAN.4: 13 residues within 4Å: Chain A: E.213, V.256, N.264, N.378, G.380, Q.440, C.445, V.446, S.447 Chain F: X.51, X.52, X.53 Ligands: NAG.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.446

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.12: 10 residues within 4Å: Chain C: S.211, E.213, P.214, V.256, L.263, N.264, G.380, V.446, S.447 Ligands: NAG.44 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.446 NAG-NAG-BMA-MAN-MAN-MAN.20: 10 residues within 4Å: Chain G: S.211, E.213, L.263, N.264, C.379, I.439, Q.440, V.446, S.447 Ligands: NAG.57 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:V.446

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

NAG.24: 4 residues within 4Å: Chain A: E.89, N.90 Chain B: G.8, S.9 Ligand excluded by PLIP NAG.25: 7 residues within 4Å: Chain A: N.236, T.238, S.276, E.277, N.278, I.279 Ligands: NAG.27 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: D.232, K.233, N.243 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain A: N.278, I.279, T.280, N.281 Ligands: NAG.25 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: N.340, W.396 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: Q.295, N.297, R.444 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain A: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-BMA-MAN.4 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: N.303, I.324 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: Q.132, S.152, F.153, N.154 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain A: R.194, N.199, T.200 Chain C: R.310 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: N.135, K.149 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: G.355, N.356 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain A: E.270, N.291, E.292 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain A: N.364, S.365, S.389 Ligands: NAG-NAG.2, NAG-NAG.2 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain B: N.99 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: K.114, E.115, N.118 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain C: N.236, T.238, G.239, S.276, E.277 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.243 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.278, N.281 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: N.340, E.341, W.396 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: N.264, N.448 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.12 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.303, I.324, V.442 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: Q.132, S.152, F.153, N.154 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.199 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.135 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain C: R.351, G.355, N.356 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain C: E.270, N.291, K.345 Ligand excluded by PLIP NAG.51: 7 residues within 4Å: Chain C: N.364, S.365, S.366, T.373 Ligands: NAG-NAG.8, NAG-NAG.9, NAG-NAG.9 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain D: E.115, N.118, Y.119 Ligand excluded by PLIP NAG.53: 6 residues within 4Å: Chain G: N.236, T.238, S.276, E.277, N.278, I.279 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain G: T.242, N.243 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain G: N.278, T.280, N.281 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain G: N.340, T.395, W.396 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain G: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.20 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain G: N.303, I.324, V.442 Ligand excluded by PLIP NAG.59: 6 residues within 4Å: Chain G: V.136, N.138, N.150, Y.167, L.169, D.322 Ligand excluded by PLIP NAG.60: 4 residues within 4Å: Chain G: Q.132, S.152, F.153, N.154 Ligand excluded by PLIP NAG.61: 5 residues within 4Å: Chain G: N.135, R.145, G.146, Q.177, Y.193 Ligand excluded by PLIP NAG.62: 1 residues within 4Å: Chain G: N.356 Ligand excluded by PLIP NAG.63: 4 residues within 4Å: Chain G: E.270, E.271, N.291, E.292 Ligand excluded by PLIP NAG.64: 3 residues within 4Å: Chain H: N.99, S.101, E.102 Ligand excluded by PLIP NAG.65: 2 residues within 4Å: Chain H: N.118, 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

BG505 SOSIP.v5.2 N241/N289 - gp120: ACG
BG505 SOSIP.v5.2 N241/N289 - gp41: BDH
Rh.33311 pAbC-4 - Heavy Chain: E
Rh.33311 pAbC-4 - Light Chain: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

G
E

B
B

D
D

H
F

E
H

F
L

BG505 SOSIP.v5.2 N241/N289 - gp120

BG505 SOSIP.v5.2 N241/N289 - gp41

Rh.33311 pAbC-4 - Heavy Chain

Rh.33311 pAbC-4 - Light Chain

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