SMTL ID : 7l8t.1

BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-1 from animal Rh.33311 (Wk26 time point)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

9 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.387, S.389, R.419 Ligands: NAG.28 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: V.136, N.138, N.150, Y.167, L.169, D.322 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.167 NAG-NAG.4: 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: 2 residues within 4Å: Chain B: N.100, T.102 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain C: S.389, N.393 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain C: N.297, T.299, H.331, N.333 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain C: V.136, N.138, N.150, Y.167, D.322 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.167 NAG-NAG.10: 4 residues within 4Å: Chain E: N.387, S.389 Ligands: NAG.53, NAG.64 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain E: V.136, N.138, N.150, Y.167, D.322 No protein-ligand interaction detected (PLIP)

1 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.2: 12 residues within 4Å: Chain A: K.66, S.211, E.213, V.256, L.263, N.264, F.377, G.380, C.445, V.446, S.447 Ligands: NAG.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.380, A:V.446

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.8: 10 residues within 4Å: Chain C: E.213, P.214, V.256, L.263, N.264, G.380, C.445, V.446, S.447 Ligands: NAG.38 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.380, C:V.446 NAG-NAG-BMA-MAN-MAN.11: 10 residues within 4Å: Chain E: E.213, L.263, N.264, F.377, C.379, G.380, C.445, V.446, S.447 Ligands: NAG.57 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:V.446 Hydrogen bonds: E:G.380, E:V.446

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

NAG.13: 6 residues within 4Å: Chain A: N.90 Chain B: G.16, T.18, N.114, T.116, Q.119 Ligand excluded by PLIP NAG.14: 6 residues within 4Å: Chain A: N.236, T.238, S.276, E.277, N.278, I.279 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.243 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.278, T.280 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: S.389, G.390, N.393 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.340, W.396 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: N.297, V.334, S.335, R.444 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.2 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.303, I.324, V.442 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: Q.132, S.152, F.153, N.154 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: R.194, N.199 Chain E: R.310 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.135 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain A: N.356 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: E.269, E.270, N.291 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: N.139, G.325 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain A: N.364, S.365, N.387 Ligands: NAG-NAG.1, NAG-NAG.1 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.107, S.109, E.110 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.126 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain C: E.89, N.90 Chain D: G.16, S.17 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: N.236, G.237, S.276 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: D.232, T.242, N.243 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.278, T.280, N.281 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.387, S.389 Ligands: NAG.45 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.340 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain C: Q.295, N.297, N.333, S.335, R.444 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.264, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.8 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.303, I.324 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: Q.132, S.152, F.153, N.154 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain A: R.310 Chain C: V.176, R.194, N.199, T.200 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.135 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.356 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: E.270, N.291, E.292 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain C: N.364, S.365, N.387 Ligands: NAG.35 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain D: N.107, S.109, E.110 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain D: N.126, Y.127 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain D: N.100, T.102 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain E: E.89, N.90 Chain F: G.16, S.17 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain E: N.236, T.238, S.276, I.279 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain E: D.232, T.242, N.243 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain E: N.278, N.281 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain E: G.390, N.393 Ligands: NAG-NAG.10 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain E: N.340 Ligand excluded by PLIP NAG.55: 5 residues within 4Å: Chain E: N.297, T.299, H.331, N.333, R.444 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain E: Q.295, N.297, N.333, S.335 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain E: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.11 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain E: N.303, I.324, V.442 Ligand excluded by PLIP NAG.59: 4 residues within 4Å: Chain E: Q.132, S.152, F.153, N.154 Ligand excluded by PLIP NAG.60: 4 residues within 4Å: Chain C: R.310 Chain E: R.194, N.199, T.200 Ligand excluded by PLIP NAG.61: 3 residues within 4Å: Chain E: N.135, T.137, K.149 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain E: K.352, N.356 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain E: E.269, N.291, K.345 Ligand excluded by PLIP NAG.64: 5 residues within 4Å: Chain E: N.364, S.365, S.366 Ligands: NAG-NAG.10, NAG-NAG.10 Ligand excluded by PLIP NAG.65: 2 residues within 4Å: Chain F: S.125, N.126 Ligand excluded by PLIP NAG.66: 2 residues within 4Å: Chain F: N.100, T.102 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-1 - Heavy Chain: G
Rh.33311 pAbC-1 - 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-1 - Heavy Chain

Rh.33311 pAbC-1 - Light Chain

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