SMTL ID : 7l8e.1

BG505 SOSIP.v5.2(7S) in complex with the polyclonal Fab pAbC-1 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: 8 residues within 4Å: Chain A: E.213, V.256, L.263, N.264, G.380, V.446, S.447 Ligands: NAG-NAG.2 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.9: 8 residues within 4Å: Chain C: E.213, V.256, L.263, N.264, G.380, V.446, S.447 Ligands: NAG-NAG.10 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.380 NAG-NAG-BMA-MAN-MAN.16: 8 residues within 4Å: Chain E: S.211, E.213, V.256, N.264, N.378, V.446, S.447 Ligands: NAG-NAG.17 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.446

18 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: 4 residues within 4Å: Chain A: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.1 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: Q.295, N.297, N.333 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: W.98, N.236, T.238, S.276 Ligands: NAG.23 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: R.194, N.199, T.200 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 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.7: 3 residues within 4Å: Chain A: N.303, I.324, V.442 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain A: N.297, T.299, H.331, N.333, S.413, T.415 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.9 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: N.297, N.333 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain C: V.176, R.194, I.196, N.199, T.200 Chain E: R.310 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.176, C:I.196 NAG-NAG.13: 3 residues within 4Å: Chain C: N.150, Y.167, L.169 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.167 NAG-NAG.14: 3 residues within 4Å: Chain C: H.87, T.242, N.243 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 6 residues within 4Å: Chain C: N.297, T.299, H.331, N.333, T.415, R.444 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain E: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.16 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 6 residues within 4Å: Chain A: R.310 Chain E: V.176, R.194, I.196, N.199, T.200 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.196 NAG-NAG.19: 2 residues within 4Å: Chain E: N.303, V.442 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain E: E.89, N.90 Chain F: G.527, S.528 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 6 residues within 4Å: Chain E: N.297, T.299, H.331, N.333, T.415, R.444 No protein-ligand interaction detected (PLIP)

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

NAG.22: 4 residues within 4Å: Chain A: Q.132, S.152, F.153, N.154 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: N.278, T.280, N.281 Ligands: NAG-NAG.4 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain A: T.373, T.374, N.387, S.389 Ligands: NAG.25 Ligand excluded by PLIP NAG.25: 6 residues within 4Å: Chain A: N.364, S.365, S.366, G.367, T.373 Ligands: NAG.24 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: C.133, T.134, N.135, Y.193 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain A: E.89, N.90 Chain B: G.524, G.527, S.528 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: H.87, K.233, N.243 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain A: E.270, E.271, N.291, E.292 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: K.336, N.340, W.396 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain A: N.356 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: S.389, N.393 Ligand excluded by PLIP NAG.33: 6 residues within 4Å: Chain B: K.633, E.634, I.635, S.636, N.637, Y.638 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: N.611, S.613 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: S.152, F.153, N.154, K.165 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: N.278, I.279, T.280, N.281 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain C: T.373, T.374, N.387, S.389 Ligands: NAG.38 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain C: N.364, S.365, S.366, T.373 Ligands: NAG.37 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain C: N.236, T.238, S.276, E.277, I.279 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: N.135, G.146, R.172 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: N.303, I.324, V.442 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: E.89, N.90 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain C: E.269, E.270, N.291, K.345 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain C: N.340, S.394, T.395, W.396 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.356 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: S.389, G.390, N.393 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: N.138, N.139 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain D: I.635, S.636, N.637 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain D: N.618, E.621 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain D: N.611, S.613 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain E: Q.132, S.152, F.153, N.154 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain E: N.278, T.280, N.281 Ligand excluded by PLIP NAG.53: 6 residues within 4Å: Chain E: Q.295, N.297, N.333, S.335, S.413, R.444 Ligand excluded by PLIP NAG.54: 6 residues within 4Å: Chain E: T.373, T.374, N.387, S.389, R.419 Ligands: NAG.55 Ligand excluded by PLIP NAG.55: 6 residues within 4Å: Chain E: N.364, S.365, S.366, G.367, T.373 Ligands: NAG.54 Ligand excluded by PLIP NAG.56: 5 residues within 4Å: Chain E: N.236, T.238, S.276, E.277, I.279 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain E: N.135, K.191 Chain H: X.88 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain E: K.231, N.243 Ligand excluded by PLIP NAG.59: 4 residues within 4Å: Chain E: E.269, E.270, E.271, N.291 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain E: K.336, N.340, W.396 Ligand excluded by PLIP NAG.61: 1 residues within 4Å: Chain E: N.356 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain E: S.389, N.393 Ligand excluded by PLIP NAG.63: 2 residues within 4Å: Chain F: S.636, N.637 Ligand excluded by PLIP NAG.64: 3 residues within 4Å: Chain F: N.618, S.620, E.621 Ligand excluded by PLIP NAG.65: 2 residues within 4Å: Chain F: N.611, S.613 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-1 Heavy Chain: G
Rh.33172 pAbC-1 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-1 Heavy Chain

Rh.33172 pAbC-1 Light Chain

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