SMTL ID : 6vl5.1

BG505 SOSIP reconstructed from a designed tetrahedral nanoparticle, BG505 SOSIP-T33_dn2

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: 9 residues within 4Å: Chain A: H.68, E.213, V.256, L.263, N.264, C.445, V.446, S.447 Ligands: NAG-NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.446 NAG-NAG-BMA-MAN-MAN.11: 9 residues within 4Å: Chain C: H.68, E.213, V.256, L.263, N.264, C.445, V.446, S.447 Ligands: NAG-NAG.12 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.446 NAG-NAG-BMA-MAN-MAN.21: 9 residues within 4Å: Chain E: H.68, E.213, V.256, L.263, N.264, C.445, V.446, S.447 Ligands: NAG-NAG.22 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:V.446

27 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: 5 residues within 4Å: Chain A: N.297, N.333, S.335, N.411, V.446 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: W.98, N.236, T.238, S.276 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: R.194, N.199, T.200 Chain C: R.310 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: 4 residues within 4Å: Chain A: E.89, N.90 Chain B: G.23, S.24 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain A: H.87, N.243, V.244 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain A: N.297, T.299, H.331, N.333, R.444 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.11 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain C: N.297, N.333, S.335, N.411, V.446 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: W.98, N.236, T.238, S.276 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain C: R.194, N.199, T.200 Chain E: R.310 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 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.17: 3 residues within 4Å: Chain C: N.303, I.324, V.442 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain C: E.89, N.90 Chain D: G.23, S.24 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain C: H.87, N.243, V.244 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 5 residues within 4Å: Chain C: N.297, T.299, H.331, N.333, R.444 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain E: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.21 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain E: N.297, N.333, S.335, N.411, V.446 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain E: W.98, N.236, T.238, S.276 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain A: R.310 Chain E: R.194, N.199, T.200 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 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.27: 3 residues within 4Å: Chain E: N.303, I.324, V.442 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain E: E.89, N.90 Chain F: G.23, S.24 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain E: H.87, N.243, V.244 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 5 residues within 4Å: Chain E: N.297, T.299, H.331, N.333, R.444 No protein-ligand interaction detected (PLIP)

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

NAG.31: 5 residues within 4Å: Chain A: S.152, F.153, N.154, K.165, Y.167 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: E.277, N.278, T.280, N.281 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain A: T.373, N.387, S.389 Ligands: NAG.34 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain A: N.364, S.365, G.367, T.373 Ligands: NAG.33 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain A: C.133, T.134, N.135, K.149, Y.193 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain A: E.270, E.271, N.291, E.292 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain A: A.337, N.340 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain A: N.356 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: S.389, G.390, N.393 Ligand excluded by PLIP NAG.40: 6 residues within 4Å: Chain B: K.129, E.130, I.131, S.132, N.133, Y.134 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: N.114, S.116, E.117 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain B: P.105, W.106, N.107, S.109 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain C: S.152, F.153, N.154, K.165, Y.167 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain C: E.277, N.278, T.280, N.281 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain C: T.373, N.387, S.389 Ligands: NAG.46 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain C: N.364, S.365, G.367, T.373 Ligands: NAG.45 Ligand excluded by PLIP NAG.47: 5 residues within 4Å: Chain C: C.133, T.134, N.135, K.149, Y.193 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain C: E.270, E.271, N.291, E.292 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: A.337, N.340 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.356 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: S.389, G.390, N.393 Ligand excluded by PLIP NAG.52: 6 residues within 4Å: Chain D: K.129, E.130, I.131, S.132, N.133, Y.134 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain D: N.114, S.116, E.117 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain D: P.105, W.106, N.107, S.109 Ligand excluded by PLIP NAG.55: 5 residues within 4Å: Chain E: S.152, F.153, N.154, K.165, Y.167 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain E: E.277, N.278, T.280, N.281 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain E: T.373, N.387, S.389 Ligands: NAG.58 Ligand excluded by PLIP NAG.58: 5 residues within 4Å: Chain E: N.364, S.365, G.367, T.373 Ligands: NAG.57 Ligand excluded by PLIP NAG.59: 5 residues within 4Å: Chain E: C.133, T.134, N.135, K.149, Y.193 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: 2 residues within 4Å: Chain E: A.337, N.340 Ligand excluded by PLIP NAG.62: 1 residues within 4Å: Chain E: N.356 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain E: S.389, G.390, N.393 Ligand excluded by PLIP NAG.64: 6 residues within 4Å: Chain F: K.129, E.130, I.131, S.132, N.133, Y.134 Ligand excluded by PLIP NAG.65: 3 residues within 4Å: Chain F: N.114, S.116, E.117 Ligand excluded by PLIP NAG.66: 4 residues within 4Å: Chain F: P.105, W.106, N.107, S.109 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martin, J.T. et al., Targeting HIV Env immunogens to B cell follicles in nonhuman primates through immune complex or protein nanoparticle formulations. NPJ Vaccines (2020)

Release Date

2020-08-12

Peptides

BG505 SOSIP.v5.2(7S) - gp120: ACE
BG505 SOSIP.v5.2(7S) - gp41: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
A

E
E

B
D

D
B

F
F

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

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

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