SMTL ID : 7l8g.1

BG505 SOSIP.v5.2(7S) in complex with the polyclonal Fab pAbC-3 from animal Rh.33172 (Wk38 time point)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-1-mer

Ligands

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.1: 6 residues within 4Å: Chain A: L.263, N.264, G.380, V.446, S.447 Ligands: NAG-NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.380 NAG-NAG-BMA-MAN-MAN.10: 8 residues within 4Å: Chain C: P.214, V.256, L.263, N.264, G.380, V.446, S.447 Ligands: NAG-NAG.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.380 NAG-NAG-BMA-MAN-MAN.17: 7 residues within 4Å: Chain E: P.214, L.263, N.264, G.380, V.446, S.447 Ligands: NAG-NAG.18 No protein-ligand interaction detected (PLIP)

22 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 5 residues within 4Å: Chain A: N.264, S.293, Q.295, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.1 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: N.297, N.333, V.334, S.335, N.411, V.446 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.411 NAG-NAG.4: 4 residues within 4Å: Chain A: N.236, T.238, S.276, I.279 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: R.194, N.199, T.200 Chain C: R.310 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain A: N.150, Y.167, L.169, G.321, D.322 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.167 NAG-NAG.7: 4 residues within 4Å: Chain A: E.89, N.90 Chain B: G.527, S.528 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain A: H.87, N.243 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 6 residues within 4Å: Chain A: N.297, T.299, H.331, N.333, T.415, R.444 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.10 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain C: N.297, N.333, V.334, S.335, R.444 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain C: R.194, I.196, N.199, T.200 Chain E: R.310 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.196 NAG-NAG.14: 4 residues within 4Å: Chain C: V.136, N.150, Y.167, D.322 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.167 NAG-NAG.15: 2 residues within 4Å: Chain C: H.87, N.243 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 6 residues within 4Å: Chain C: N.297, T.299, H.331, N.333, N.411, T.415 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain E: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.17 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain E: Q.295, N.297, N.333, N.411, R.444 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.411, E:N.411 NAG-NAG.20: 4 residues within 4Å: Chain A: R.310 Chain E: R.194, N.199, T.200 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 6 residues within 4Å: Chain E: N.303, I.324, V.442 Chain H: X.48, X.49, X.50 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain E: E.89, N.90 Chain F: S.528 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain E: H.87, K.231, N.243 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 5 residues within 4Å: Chain E: N.297, T.299, H.331, N.333, T.415 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain E: S.152, F.153, N.154 No protein-ligand interaction detected (PLIP)

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

NAG.26: 4 residues within 4Å: Chain A: S.152, F.153, N.154, K.165 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: N.278, T.280, N.281 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain A: T.373, N.387, S.389 Ligands: NAG.29 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain A: N.364, S.365, G.367 Ligands: NAG.28 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: N.135, R.145, G.146 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: N.303, I.324, V.442 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: E.270, E.271, N.291, E.292 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain A: K.336, A.337, N.340, W.396 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain A: N.356 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain A: N.393 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain B: K.633, E.634, S.636, N.637, Y.638 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: N.618, E.621 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain B: P.609, W.610, N.611, S.613 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: S.152, F.153, N.154, K.165 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: N.278, T.280, N.281 Ligand excluded by PLIP NAG.41: 6 residues within 4Å: Chain C: T.373, T.374, N.387, S.389, R.419 Ligands: NAG.42 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain C: N.364, S.365, S.366, G.367 Ligands: NAG.41 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain C: N.236, T.238, S.276, I.279 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.135 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.303, I.324, V.442 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain C: E.270, E.271, N.291, E.292, K.345 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: K.336, N.340, W.396 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.356 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: G.390, N.393 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain D: S.636, N.637 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain D: N.618, S.620, E.621 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain D: P.609, W.610, N.611, S.613 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain E: N.278, T.280, N.281 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain E: N.387, S.389 Ligands: NAG.55 Ligand excluded by PLIP NAG.55: 4 residues within 4Å: Chain E: N.364, S.365, G.367 Ligands: NAG.54 Ligand excluded by PLIP NAG.56: 5 residues within 4Å: Chain E: W.98, N.236, T.238, S.276, I.279 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain E: N.135, R.145, G.146 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain E: E.270, E.271, N.291, E.292 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain E: N.340, W.396 Ligand excluded by PLIP NAG.60: 1 residues within 4Å: Chain E: N.356 Ligand excluded by PLIP NAG.61: 3 residues within 4Å: Chain E: S.389, G.390, N.393 Ligand excluded by PLIP NAG.62: 4 residues within 4Å: Chain F: K.633, E.634, S.636, N.637 Ligand excluded by PLIP NAG.63: 4 residues within 4Å: Chain F: N.618, S.620, E.621, N.625 Ligand excluded by PLIP NAG.64: 4 residues within 4Å: Chain F: N.611, S.613, W.614, L.645 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

Envelope glycoprotein gp160: ABCDEF
Rh.33172 pAbC-3 Heavy Chain: G
Rh.33172 pAbC-3 Light Chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

D
F

E
A

F
B

G
H

H
L

Envelope glycoprotein gp160

Rh.33172 pAbC-3 Heavy Chain

Rh.33172 pAbC-3 Light Chain

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