SMTL ID : 7l7t.1

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

Coordinates

PDB Format Compare

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: 10 residues within 4Å: Chain A: E.213, P.214, V.256, L.263, N.264, N.378, G.380, V.446, S.447 Ligands: NAG-NAG.2 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.10: 10 residues within 4Å: Chain C: E.213, P.214, V.256, L.263, N.264, N.378, G.380, V.446, S.447 Ligands: NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.19: 10 residues within 4Å: Chain E: E.213, P.214, V.256, L.263, N.264, N.378, G.380, V.446, S.447 Ligands: NAG-NAG.20 No protein-ligand interaction detected (PLIP)

24 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: 4 residues within 4Å: Chain A: R.194, I.196, N.199, T.200 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.196 NAG-NAG.5: 5 residues within 4Å: Chain A: V.136, T.137, N.138, N.150, Y.167 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: 2 residues within 4Å: Chain A: K.231, N.243 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain A: N.297, T.299, H.331, N.333, T.415 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain A: Q.132, S.152, F.153, N.154 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: 3 residues within 4Å: Chain C: Q.295, N.297, N.333 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain C: R.194, I.196, N.199, T.200 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.196 NAG-NAG.14: 5 residues within 4Å: Chain C: V.136, T.137, N.138, N.150, Y.167 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.167 NAG-NAG.15: 3 residues within 4Å: Chain C: N.303, I.324, V.442 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain C: K.231, N.243 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 5 residues within 4Å: Chain C: N.297, T.299, H.331, N.333, T.415 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain C: Q.132, S.152, F.153, N.154 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain E: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.19 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain E: Q.295, N.297, N.333 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: 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.23: 5 residues within 4Å: Chain E: V.136, T.137, N.138, N.150, Y.167 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.167 NAG-NAG.24: 3 residues within 4Å: Chain E: N.303, I.324, V.442 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain E: K.231, N.243 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 5 residues within 4Å: Chain E: N.297, T.299, H.331, N.333, T.415 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 4 residues within 4Å: Chain E: Q.132, 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.28: 2 residues within 4Å: Chain A: N.278, T.280 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: N.387, S.389 Ligands: NAG.30 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain A: N.364, S.365, G.367, T.373 Ligands: NAG.29 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: W.98, N.236, T.238, S.276 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain A: C.133, T.134, N.135, K.149, Y.193 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain A: E.89, N.90 Chain B: G.8, S.9 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain A: E.270, E.271, N.291, E.292 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: K.336, N.340, W.396 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain A: N.356 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain A: S.389, N.393 Ligand excluded by PLIP NAG.38: 6 residues within 4Å: Chain B: K.114, E.115, I.116, S.117, N.118, Y.119 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: N.99, S.101 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain B: P.90, W.91, N.92, S.94 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.278, T.280 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.387, S.389 Ligands: NAG.43 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain C: N.364, S.365, G.367, T.373 Ligands: NAG.42 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain C: W.98, N.236, T.238, S.276 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain C: C.133, T.134, N.135, K.149, Y.193 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: E.89, N.90 Chain D: G.8, S.9 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain C: E.270, E.271, N.291, E.292 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: K.336, N.340, W.396 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain C: N.356 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: S.389, N.393 Ligand excluded by PLIP NAG.51: 6 residues within 4Å: Chain D: K.114, E.115, I.116, S.117, N.118, Y.119 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain D: N.99, S.101 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain D: P.90, W.91, N.92, S.94 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain E: N.278, T.280 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain E: N.387, S.389 Ligands: NAG.56 Ligand excluded by PLIP NAG.56: 5 residues within 4Å: Chain E: N.364, S.365, G.367, T.373 Ligands: NAG.55 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain E: W.98, N.236, T.238, S.276 Ligand excluded by PLIP NAG.58: 5 residues within 4Å: Chain E: C.133, T.134, N.135, K.149, Y.193 Ligand excluded by PLIP NAG.59: 4 residues within 4Å: Chain E: E.89, N.90 Chain F: G.8, S.9 Ligand excluded by PLIP NAG.60: 4 residues within 4Å: Chain E: E.270, E.271, N.291, E.292 Ligand excluded by PLIP NAG.61: 3 residues within 4Å: Chain E: K.336, N.340, W.396 Ligand excluded by PLIP NAG.62: 1 residues within 4Å: Chain E: N.356 Ligand excluded by PLIP NAG.63: 2 residues within 4Å: Chain E: S.389, N.393 Ligand excluded by PLIP NAG.64: 6 residues within 4Å: Chain F: K.114, E.115, I.116, S.117, N.118, Y.119 Ligand excluded by PLIP NAG.65: 2 residues within 4Å: Chain F: N.99, S.101 Ligand excluded by PLIP NAG.66: 4 residues within 4Å: Chain F: P.90, W.91, N.92, S.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(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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