SMTL ID : 9nhm.1

BG505-CH505 Env glycoprotein in complex with NHP pAb V1V2V3-1 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: 5 residues within 4Å: Chain C: E.88, 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.31 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.45 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: 9 residues within 4Å: Chain C: E.207, V.250, L.257, N.258, F.370, N.371, V.439, S.440 Ligands: NAG.15 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 8 residues within 4Å: Chain E: P.208, V.250, L.257, N.258, N.371, G.373, V.439 Ligands: NAG.37 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 5 residues within 4Å: Chain G: E.207, N.258, N.371, V.439, S.440 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:V.439 Hydrogen bonds: 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: 3 residues within 4Å: Chain B: X.31 Chain C: N.297, G.434 No protein-ligand interaction detected (PLIP)

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

NAG.8: 4 residues within 4Å: Chain C: N.135, Q.186 Ligands: NAG.9, NAG.19 Ligand excluded by PLIP NAG.9: 5 residues within 4Å: Chain C: S.154, F.155, N.156, K.167 Ligands: NAG.8 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain C: N.193, T.194 Chain G: R.304 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain C: N.226, N.236 Ligands: NAG-NAG-NAG.1 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain C: G.264, N.285, E.286 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain C: T.366, T.367, N.380 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain C: N.435, I.436, T.437 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain C: L.261, S.287, N.441 Ligands: NAG-NAG-BMA.2, NAG-NAG-BMA.2 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain C: N.138, E.148 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain C: F.355, N.386, S.387 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain C: K.351, N.352 Ligand excluded by PLIP NAG.19: 7 residues within 4Å: Chain A: X.26, X.27 Chain C: N.135, N.152, S.154, N.169 Ligands: NAG.8 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain C: E.291, Y.325, N.327, S.406, T.408 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain C: N.334, S.387, W.389 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain C: N.272, T.274 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain D: Q.141, Q.142, N.145 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain D: N.100, T.102, W.103, I.130 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain D: N.126, Y.127 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain D: N.105, K.106 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain E: N.135, Q.186 Ligands: NAG.29 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain E: T.137, N.152, C.153, S.154, N.169 Ligand excluded by PLIP NAG.29: 6 residues within 4Å: Chain E: T.133, L.134, N.135, S.154, N.156 Ligands: NAG.27 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain E: V.178, R.188, I.190, N.193 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain E: N.226, T.228, N.237 Ligands: NAG-NAG-NAG.4 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain E: E.265, N.285, E.286 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain E: N.297, N.435 Ligand excluded by PLIP NAG.34: 6 residues within 4Å: Chain E: R.322, Y.325, N.327, D.405, S.406, T.408 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain E: T.366, T.367, N.380, S.382 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain E: N.435, I.436, T.437 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain E: L.261, S.287, N.441 Ligands: NAG-NAG-BMA.5 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain E: N.93 Chain F: G.16, T.18, T.116 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain E: N.352, T.388, W.389 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain F: Q.141, N.145 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain G: N.135, S.185, Q.186 Ligands: NAG.43 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain G: A.139, T.140, N.152, L.171, Q.316 Ligand excluded by PLIP NAG.43: 6 residues within 4Å: Chain G: T.133, L.134, N.135, S.154, N.156 Ligands: NAG.41 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain G: V.178, Q.179, R.188, N.193 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain G: N.226, T.228, N.237 Ligands: NAG-NAG-NAG.6 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain G: E.265, N.285, E.286 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain G: N.297 Ligand excluded by PLIP NAG.48: 5 residues within 4Å: Chain G: T.293, Y.325, N.327, S.406, T.408 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain G: N.435, I.436, T.437 Ligand excluded by PLIP NAG.50: 5 residues within 4Å: Chain G: S.287, V.288, K.289, S.440, N.441 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain G: E.92, N.93 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain G: N.138, S.145, K.151 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain G: T.366, T.367, N.380 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain G: N.352, T.388, W.389 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-V1V2V3-1 pAb heavy chain: A
RUu-V1V2V3-1 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-V1V2V3-1 pAb heavy chain

RUu-V1V2V3-1 pAb light chain

BG505-CH505 Envelope glycoprotein gp120

BG505-CH505 Transmembrane protein gp41

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