SMTL ID : 9nho.1

BG505-CH505 Env glycoprotein in complex with NHP pAb V1V2V3-5 isolated from animal RUu18 at week 14

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.80 Å

Oligo State

hetero-1-1-3-3-mer

Ligands

3 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG.1: 6 residues within 4Å: Chain C: E.88, V.90, N.225, N.237, S.239 Ligands: NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.4: 6 residues within 4Å: Chain E: E.88, V.90, N.225, N.237, S.239 Ligands: NAG.26 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.6: 6 residues within 4Å: Chain G: E.88, V.90, N.225, N.237, S.239 Ligands: NAG.40 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 8 residues within 4Å: Chain C: E.207, L.257, N.258, N.371, G.373, V.439, S.440 Ligands: NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 8 residues within 4Å: Chain E: E.207, V.250, L.257, N.258, G.373, V.439, S.440 Ligands: NAG.32 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.373 NAG-NAG-BMA.7: 8 residues within 4Å: Chain G: E.207, P.208, V.250, L.257, N.258, T.437, V.439, S.440 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:V.439 Hydrogen bonds: G:E.207, G:V.439

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 4 residues within 4Å: Chain C: N.327, S.406, I.407, T.408 No protein-ligand interaction detected (PLIP)

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

NAG.8: 3 residues within 4Å: Chain C: N.135, Q.186 Ligands: NAG.9 Ligand excluded by PLIP NAG.9: 5 residues within 4Å: Chain C: T.133, N.135, N.156, Q.186 Ligands: NAG.8 Ligand excluded by PLIP NAG.10: 5 residues within 4Å: Chain C: V.178, Q.179, R.188, N.193, T.194 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain C: N.226, T.228 Ligands: NAG-NAG-NAG.1 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain C: E.265, N.285, E.286 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain C: N.297, N.435 Ligands: NAG.15 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain C: T.366, T.367, N.380, S.382 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain C: N.435, T.437 Ligands: NAG.13 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain C: L.261, S.287, N.441 Ligands: NAG-NAG-BMA.2 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain C: N.143, S.144 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain C: T.137, N.138 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain C: P.357, N.386 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain C: E.330, N.334, W.389 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain D: N.105, K.106 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain D: N.100, T.102, W.103, L.134 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain E: N.135, S.185, Q.186 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain E: A.139, T.140, N.152, L.171, Q.316 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain E: S.154, F.155, N.156 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain E: N.226, T.228 Ligands: NAG-NAG-NAG.4 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain E: N.285, E.286 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain E: N.297, Q.433, G.434 Ligands: NAG.31 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain E: E.291, Y.325, N.327, S.406, T.408 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain E: S.358, T.366, T.367, N.380, S.382 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain E: N.435, I.436, T.437 Ligands: NAG.28 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain E: L.261, S.287, N.441 Ligands: NAG-NAG-BMA.5, NAG-NAG-BMA.5 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain E: N.93 Chain F: T.116, Q.119 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain E: N.352, T.388, W.389 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain F: Q.141, N.145 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain F: P.98, W.99, N.100 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain G: N.135, C.136, T.137 Ligand excluded by PLIP NAG.38: 6 residues within 4Å: Chain G: A.139, T.140, A.141, N.152, L.171, Q.316 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain G: S.154, F.155, N.156 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain G: N.226, T.228, N.237 Ligands: NAG-NAG-NAG.6 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain G: E.265, N.285, E.286 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain G: N.297, I.318 Ligands: NAG.44 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain G: Y.325, N.327, S.406, T.408 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain G: N.435, T.437 Ligands: NAG.42 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain G: K.248, S.287, N.441 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain G: T.137, N.138, I.146, K.151 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain H: P.98, N.100, T.102 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pratap, P.P. et al., Immunofocusing on the conserved fusion peptide of HIV envelope glycoprotein in rhesus macaques. Biorxiv (2024)

Release Date

2025-06-25

Peptides

V1V2V3-5 pAb Heavy Chain: A
V1V2V3-5 pAb Light Chain: B
BG505-CH505 Envelope glycoprotein gp120: CEG
BG505-CH505 Transmembrane protein gp41: DFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
C

E
A

G
E

D
D

F
B

H
F

V1V2V3-5 pAb Heavy Chain

V1V2V3-5 pAb Light Chain

BG505-CH505 Envelope glycoprotein gp120

BG505-CH505 Transmembrane protein gp41

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