SMTL ID : 7l8w.1

BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-3 from animal Rh.33311 (Wk26 time point)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-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-MAN-MAN.1: 19 residues within 4Å: Chain A: E.213, L.263, N.264, N.378, C.379, G.380, I.439, Q.440, R.444, C.445, V.446, S.447 Chain G: X.25, X.26, X.27, X.30, X.93, X.94 Ligands: NAG.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.444, A:G.380, A:V.446 Hydrophobic interactions: A:V.446

5 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.138, N.150, L.169, D.322 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain C: N.297, C.298, T.299, H.331, N.333, T.415, R.444 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain C: N.150, D.322 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain E: N.297, T.299, H.331, N.333, R.444 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain E: V.136, N.138, N.150, Y.167, L.169, D.322 No protein-ligand interaction detected (PLIP)

2 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.4: 12 residues within 4Å: Chain C: S.211, E.213, P.214, V.256, L.263, N.264, N.378, G.380, C.445, V.446, S.447 Ligands: NAG.36 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.446 Hydrogen bonds: C:V.446 NAG-NAG-BMA-MAN-MAN.7: 8 residues within 4Å: Chain E: S.211, E.213, V.256, L.263, N.264, V.446, S.447 Ligands: NAG.55 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:V.446 Hydrogen bonds: E:V.446

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

NAG.9: 4 residues within 4Å: Chain A: E.89, N.90 Chain B: G.8, S.9 Ligand excluded by PLIP NAG.10: 6 residues within 4Å: Chain A: N.236, T.238, S.276, E.277, N.278, I.279 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: H.87, K.231, N.243 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.278, T.280, N.281 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: S.389, N.393 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.387, S.389 Ligands: NAG.25 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: N.340, S.394, T.395, W.396 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: N.297, T.299, H.331, N.333 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain A: Q.295, N.297, N.333, V.334, S.335 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.1 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.303, I.324, V.442 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: T.130, Q.132, F.153, N.154 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: R.194, N.199, T.200 Chain E: R.310 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: N.135, R.145, K.149, Y.193 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: E.270, N.291, K.345 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.139 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain A: N.364, S.365, T.373 Ligands: NAG.14 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: P.90, W.91, N.92, T.94 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.118, Y.119 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: 5 residues within 4Å: Chain C: F.235, N.236, G.237, T.238, G.239 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: K.231, D.232, N.243 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: N.278, I.279, T.280 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: S.389, G.390, N.393 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain C: T.374, N.387, S.389 Ligands: NAG.43 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: K.336, N.340, W.396 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain C: Q.295, N.297, N.333, S.335, R.444 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.4 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.303, I.324, V.442 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain C: Q.132, S.152, F.153, N.154 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: R.310 Chain C: R.194, N.199 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: N.135, R.145, 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, E.271, N.291, E.292 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain C: N.364, S.365, S.366 Ligands: NAG.33 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain D: N.99, S.101 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain D: N.118 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain D: N.92, T.94, W.95 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain E: E.89, N.90 Chain F: G.8, S.9 Ligand excluded by PLIP NAG.48: 6 residues within 4Å: Chain E: N.236, T.238, S.276, E.277, N.278, I.279 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain E: D.232, T.242, N.243 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain E: N.278, T.280, N.281 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain E: N.393 Ligands: NAG.52, NAG.62 Ligand excluded by PLIP NAG.52: 5 residues within 4Å: Chain E: N.387, S.389, R.419 Ligands: NAG.51, NAG.62 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain E: N.340, W.396 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain E: Q.295, N.297, R.444, V.446 Ligand excluded by PLIP NAG.55: 4 residues within 4Å: Chain E: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.7 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain E: N.303, G.441, V.442 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain E: Q.132, S.152, F.153, N.154 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain C: R.310 Chain E: R.194, N.199, T.200 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain E: N.135, R.145 Ligand excluded by PLIP NAG.60: 4 residues within 4Å: Chain E: R.351, K.352, G.355, N.356 Ligand excluded by PLIP NAG.61: 4 residues within 4Å: Chain E: E.270, E.271, N.291, E.292 Ligand excluded by PLIP NAG.62: 5 residues within 4Å: Chain E: N.364, S.366, N.387 Ligands: NAG.51, NAG.52 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain F: N.99, S.101, E.102 Ligand excluded by PLIP NAG.64: 4 residues within 4Å: Chain F: K.114, E.115, S.117, N.118 Ligand excluded by PLIP NAG.65: 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-3 - Heavy Chain: G
Rh.33311 pAbC-3 - 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-3 - Heavy Chain

Rh.33311 pAbC-3 - Light Chain

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