SMTL ID : 9nhk.1

BG505-CH505 Env glycoprotein in complex with NHP pAb Base-4 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- 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.1: 9 residues within 4Å: Chain C: P.208, V.250, L.257, N.258, F.370, C.372, C.438, V.439, S.440 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:C.372 NAG-NAG-BMA.3: 8 residues within 4Å: Chain E: E.207, P.208, V.250, L.257, N.258, V.439, S.440 Ligands: NAG.33 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:V.439 Hydrogen bonds: E:E.207, E:V.439 NAG-NAG-BMA.5: 8 residues within 4Å: Chain G: E.207, V.250, L.257, N.258, G.373, V.439, S.440 Ligands: NAG.52 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:G.373

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.2: 6 residues within 4Å: Chain E: E.88, V.90, N.225, N.237, S.239 Ligands: NAG.27 No protein-ligand interaction detected (PLIP)

1 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.4: 6 residues within 4Å: Chain G: E.88, V.90, N.225, N.237, S.239 Ligands: NAG.47 No protein-ligand interaction detected (PLIP)

55 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.6: 3 residues within 4Å: Chain C: N.135, S.185, Q.186 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain C: T.140, N.152, G.315 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain C: S.154, F.155, N.156 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain C: V.178, Q.179, R.188, N.193 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain C: N.226, T.228 Ligands: NAG.11 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain C: N.225, N.237 Ligands: NAG.10 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain C: E.265, N.285, E.286 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain C: N.297, G.434, N.435 Ligands: NAG.16 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain C: R.322, Y.325, N.327, S.406, T.408 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain C: T.366, T.367, N.380, S.382, R.412 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain C: N.435, I.436, T.437 Ligands: NAG.13 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain C: S.287, V.288, K.289, S.440, N.441 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain C: T.137, N.138, I.146 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain C: E.92, N.93 Chain D: T.18 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain C: N.334, E.335, W.389 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain D: Q.141, Q.142, N.145 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain D: N.100, S.101, T.102, W.103 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: T.140, N.152, N.169, A.170, L.171 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain E: S.154, F.155, N.156, K.167 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain E: V.178, R.188, N.193 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain E: N.226, T.228, N.236 Ligands: NAG-NAG.2 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain E: G.264, E.265, N.285, E.286 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain E: N.297, I.318 Ligands: NAG.32 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain E: Y.325, N.327, S.406, I.407, T.408 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain E: T.366, T.367, N.380, S.382 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain E: N.297, N.435, T.437 Ligands: NAG.29 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain E: L.261, S.287, N.441 Ligands: NAG-NAG-BMA.3 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 E: P.357, N.386 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain E: N.272, T.274 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain E: N.93 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain E: T.137, N.138, I.146, K.151 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain F: N.100, T.102 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain F: K.122, E.123, S.125, N.126 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain F: N.105 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain F: Q.141, Q.142, N.145 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain G: N.135, S.185, Q.186 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain G: A.139, T.140, N.152, L.171, Q.316 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain G: S.154, F.155, N.156 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain E: R.304 Chain G: R.188, I.190, N.193 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain G: N.226, T.228 Ligands: NAG-NAG-NAG.4 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain G: N.285, E.286 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain G: N.297, I.318, G.319 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain G: Y.325, N.327, S.406, T.408 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain G: N.435, T.437 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain G: L.261, S.287, N.441 Ligands: NAG-NAG-BMA.5 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain G: E.92, N.93 Chain H: S.17 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain G: T.137, N.138, I.146 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain G: N.386 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain G: N.380, S.382, P.410 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain H: S.125, N.126 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain H: N.100, T.102, Y.127 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain H: Q.141, Q.142, N.145 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain H: N.105, K.106 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-Base-4 pAb heavy chain: A
RUu-Base-4 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-Base-4 pAb heavy chain

RUu-Base-4 pAb light chain

BG505-CH505 Envelope glycoprotein gp120

BG505-CH505 Transmembrane protein gp41

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