SMTL ID : 7l7u.1

BG505 SOSIP reconstructed from a designed nanoparticle, BG505 SOSIP-T33-31 (Component B)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-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: 11 residues within 4Å: Chain A: S.211, E.213, V.256, L.263, N.264, F.377, N.378, G.380, V.446, S.447 Ligands: NAG-NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.446 NAG-NAG-BMA-MAN-MAN.9: 11 residues within 4Å: Chain C: S.211, E.213, V.256, L.263, N.264, F.377, N.378, G.380, V.446, S.447 Ligands: NAG-NAG.10 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.446 NAG-NAG-BMA-MAN-MAN.17: 11 residues within 4Å: Chain E: S.211, E.213, V.256, L.263, N.264, F.377, N.378, G.380, V.446, S.447 Ligands: NAG-NAG.18 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.446

21 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: R.194, I.196, N.199, T.200 Chain C: R.310 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.196 NAG-NAG.5: 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.6: 3 residues within 4Å: Chain A: N.303, I.324, V.442 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain A: E.89, N.90 Chain B: G.5, S.9 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain A: N.297, T.299, N.333, S.413, T.415, R.444 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: 3 residues within 4Å: Chain C: Q.295, N.297, N.333 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 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.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: 3 residues within 4Å: Chain C: N.303, I.324, V.442 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain C: E.89, N.90 Chain D: G.5, S.9 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 6 residues within 4Å: Chain C: N.297, T.299, N.333, S.413, T.415, R.444 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: 3 residues within 4Å: Chain E: Q.295, N.297, N.333 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 5 residues within 4Å: Chain A: R.310 Chain E: R.194, I.196, N.199, T.200 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.196 NAG-NAG.21: 5 residues within 4Å: Chain E: V.136, N.150, Y.167, L.169, D.322 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.167 NAG-NAG.22: 3 residues within 4Å: Chain E: N.303, I.324, V.442 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain E: E.89, N.90 Chain F: G.5, S.9 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 6 residues within 4Å: Chain E: N.297, T.299, N.333, S.413, T.415, R.444 No protein-ligand interaction detected (PLIP)

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

NAG.25: 4 residues within 4Å: Chain A: Q.132, S.152, F.153, N.154 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: N.278, T.280 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: N.364, N.387, S.389 Ligands: NAG.28 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain A: N.364, S.365, G.367 Ligands: NAG.27 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: N.236, T.238, S.276 Ligand excluded by PLIP NAG.30: 6 residues within 4Å: Chain A: C.133, T.134, N.135, K.149, N.190, Y.193 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: H.87, K.231, N.243 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: E.270, N.291, E.292 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: K.336, N.340, W.396 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain A: R.351, K.352, G.355, N.356 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain B: K.114, E.115, S.117, N.118, Y.119 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.99, E.102 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: P.90, W.91, N.92 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: 2 residues within 4Å: Chain C: N.278, T.280 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: N.364, N.387, S.389 Ligands: NAG.41 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain C: N.364, S.365, G.367 Ligands: NAG.40 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.236, T.238, S.276 Ligand excluded by PLIP NAG.43: 6 residues within 4Å: Chain C: C.133, T.134, N.135, K.149, N.190, Y.193 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: H.87, K.231, N.243 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: E.270, N.291, E.292 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: K.336, N.340, W.396 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain C: R.351, K.352, G.355, N.356 Ligand excluded by PLIP NAG.48: 5 residues within 4Å: Chain D: K.114, E.115, S.117, N.118, Y.119 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain D: N.99, E.102 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain D: P.90, W.91, N.92 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: 2 residues within 4Å: Chain E: N.278, T.280 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain E: N.364, N.387, S.389 Ligands: NAG.54 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain E: N.364, S.365, G.367 Ligands: NAG.53 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain E: N.236, T.238, S.276 Ligand excluded by PLIP NAG.56: 6 residues within 4Å: Chain E: C.133, T.134, N.135, K.149, N.190, Y.193 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain E: H.87, K.231, N.243 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain E: E.270, N.291, E.292 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain E: K.336, N.340, W.396 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: 5 residues within 4Å: Chain F: K.114, E.115, S.117, N.118, Y.119 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain F: N.99, E.102 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain F: P.90, W.91, N.92 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(7S) - gp120: ACE
BG505 SOSIP.v5.2(7S) - gp41: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

BG505 SOSIP.v5.2(7S) - gp120

BG505 SOSIP.v5.2(7S) - gp41

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