SMTL ID : 9nhl.1

BG505-CH505 Env glycoprotein in complex with NHP pAb FP-1 isolated from animal RUu18 at week 14

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

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.12 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.3: 5 residues within 4Å: Chain D: E.88, V.90, N.225, N.237 Ligands: NAG.24 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.5: 7 residues within 4Å: Chain A: X.1, X.25 Chain G: E.88, V.90, N.225, N.237, S.239 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, P.208, V.250, L.257, N.258, G.373, V.439, S.440 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.439 Hydrogen bonds: C:V.439 NAG-NAG-BMA.4: 7 residues within 4Å: Chain D: E.207, L.257, N.258, G.373, V.439, S.440 Ligands: NAG.30 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.373 NAG-NAG-BMA.6: 10 residues within 4Å: Chain G: E.207, V.250, L.257, N.258, N.371, G.373, C.438, V.439, S.440 Ligands: NAG.46 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:G.373, 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.7: 6 residues within 4Å: Chain A: X.101, X.102 Chain G: N.93 Chain H: N.114, T.116 Ligands: NAG.47 No protein-ligand interaction detected (PLIP)

43 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.10 Ligand excluded by PLIP NAG.9: 5 residues within 4Å: Chain C: A.139, T.140, N.152, L.171, Q.316 Ligand excluded by PLIP NAG.10: 5 residues within 4Å: Chain C: T.133, N.135, S.154, N.156 Ligands: NAG.8 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain C: V.178, R.188, N.193 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain C: N.226, T.228 Ligands: NAG-NAG-NAG.1 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain C: E.265, N.285, E.286 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain C: N.297, N.435 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain C: Y.325, N.327, S.406, T.408 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain C: T.366, T.367, N.380, S.382 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain C: N.435, I.436, T.437 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain C: L.261, S.287, N.441 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain C: E.92, N.93 Chain E: G.16, S.17 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain D: N.135, Q.186 Ligands: NAG.22 Ligand excluded by PLIP NAG.21: 6 residues within 4Å: Chain D: A.139, T.140, N.152, L.171, G.315, Q.316 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain D: T.133, N.156, Q.186 Ligands: NAG.20 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain D: V.178, R.188, N.193 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain D: N.226, T.228, N.236 Ligands: NAG-NAG-NAG.3 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain D: E.265, N.285, E.286, K.342 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain D: N.297, I.318, G.434 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain D: Y.325, N.327, S.406, T.408 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain D: T.366, T.367, N.380, S.382, R.412 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain D: N.435, I.436, T.437 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain D: L.261, S.287, N.441 Ligands: NAG-NAG-BMA.4 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain E: P.98, W.99, N.100, T.102, W.103 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain E: S.101, N.105 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain E: Q.141, N.145, N.149 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain F: K.122, E.123, S.125, N.126 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain F: N.100, T.102 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain G: N.135, Q.186 Ligands: NAG.38 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain G: N.152, N.169, A.170, L.171 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain G: N.135, S.154, F.155, N.156 Ligands: NAG.36 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain G: R.188, N.193 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain G: N.226, T.228, N.236 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain G: E.265, N.285, E.286, K.342 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain G: N.297 Ligands: NAG.45 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain G: Y.325, N.327, S.406, I.407, T.408 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain G: T.366, T.367, N.380, S.382 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain G: T.293, P.295, N.435, T.437 Ligands: NAG.42 Ligand excluded by PLIP NAG.46: 6 residues within 4Å: Chain G: N.258, S.287, V.439, S.440, N.441 Ligands: NAG-NAG-BMA.6 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain H: N.114 Ligands: NAG-NAG.7 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain H: N.105 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain H: N.100, T.102 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain H: K.122, E.123, 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-FP-1 pAb heavy chain: A
RUu-FP-1 pAb light chain: B
BG505-CH505 Envelope glycoprotein gp120: CDG
BG505-CH505 Transmembrane protein gp41: EFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

D
Y

G
C

E
D

F
F

H
B

RUu-FP-1 pAb heavy chain

RUu-FP-1 pAb light chain

BG505-CH505 Envelope glycoprotein gp120

BG505-CH505 Transmembrane protein gp41

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