SMTL ID : 9nhn.1

BG505-CH505 Env glycoprotein in complex with NHP pAb V1V2V3-2 isolated from animal RUu18 at week 14

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.90 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.10 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.3: 5 residues within 4Å: Chain E: E.88, V.90, N.225, N.237 Ligands: NAG.26 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.5: 4 residues within 4Å: Chain G: E.88, N.225, N.237 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: 7 residues within 4Å: Chain C: E.207, P.208, V.250, L.257, N.258, G.373, V.439 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.373 NAG-NAG-BMA.4: 4 residues within 4Å: Chain E: N.258, N.371, V.439 Ligands: NAG.32 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.439 NAG-NAG-BMA.6: 9 residues within 4Å: Chain G: E.207, V.250, L.257, N.258, N.371, G.373, V.439, S.440 Ligands: NAG.45 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:G.373

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

NAG.7: 4 residues within 4Å: Chain C: N.135, S.185, Q.186 Ligands: NAG.8 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain C: F.155, N.156 Ligands: NAG.7 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain C: V.178, R.188, N.193 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain C: N.226, N.236 Ligands: NAG-NAG-NAG.1 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain C: N.285, E.286 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain C: N.297, I.318, G.434 Ligand excluded by PLIP NAG.13: 5 residues within 4Å: Chain C: T.293, Y.325, N.327, S.406, T.408 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain C: S.358, T.366, T.367, N.380, S.382 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain C: N.435, T.437 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain C: S.287, V.288, K.289, S.440, N.441 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain C: N.138, I.146, I.147, M.150, K.151 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain D: N.105 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain D: K.122, E.123, S.125, N.126 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain D: N.100, T.102, W.103, I.130 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain D: N.145 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain E: N.135, Q.186 Ligands: NAG.24 Ligand excluded by PLIP NAG.23: 6 residues within 4Å: Chain E: T.140, A.141, N.152, L.171, G.315, Q.316 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain E: T.133, N.156, Q.186 Ligands: NAG.22 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain E: V.178, R.188, N.193 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain E: N.226 Ligands: NAG-NAG-NAG.3 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain E: G.264, E.265, N.285, E.286 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain E: N.297, N.435 Ligands: NAG.31 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain E: N.327, S.406, I.407, T.408 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain E: 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: 4 residues within 4Å: Chain E: L.261, S.287, N.441 Ligands: NAG-NAG-BMA.4 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain E: E.92, N.93 Chain F: A.15, G.16, S.17 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain E: T.137, N.138, I.146 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain E: P.357, N.386 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain F: N.100, T.102 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain G: T.133, L.134, N.135, S.185, Q.186 Ligand excluded by PLIP NAG.38: 6 residues within 4Å: Chain G: A.139, T.140, N.152, L.171, G.315, Q.316 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain G: F.155, N.156, R.165, E.166, K.167 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain G: N.226, T.228, N.237 Ligands: NAG-NAG-NAG.5 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain G: N.285, E.286 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain G: N.297, N.435 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain G: R.322, Y.325, N.327, S.406, T.408 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain G: N.435, T.437 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain G: L.261, S.287, N.441 Ligands: NAG-NAG-BMA.6 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain G: E.92, N.93 Chain H: S.17 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain G: T.366, T.367, N.380 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain G: P.357, S.382, N.386 Ligand excluded by PLIP NAG.49: 5 residues within 4Å: Chain G: E.330, S.331, N.334, S.387, W.389 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain G: N.138, I.146 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain H: N.100, T.102 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain H: N.105 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain H: K.122, E.123, S.125, N.126 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

RUu-V1V2V3-2 pAb heavy chain: A
RUu-V1V2V3-2 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

RUu-V1V2V3-2 pAb heavy chain

RUu-V1V2V3-2 pAb light chain

BG505-CH505 Envelope glycoprotein gp120

BG505-CH505 Transmembrane protein gp41

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