SMTL ID : 9nhh.1

AMC016 v4.2 in complex with pAb Base-A isolated from animal RQk18 at week 43

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.00 Å

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: 3 residues within 4Å: Chain C: E.58, N.59 Chain E: S.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 4 residues within 4Å: Chain F: G.13, S.17 Chain G: E.58, N.59 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 3 residues within 4Å: Chain D: S.17 Chain H: E.58, N.59 No protein-ligand interaction detected (PLIP)

12 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 C: L.105, N.135, Y.152, T.154, G.298, Q.299 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.152 Hydrogen bonds: C:Q.299 NAG-NAG.3: 6 residues within 4Å: Chain C: T.276, H.308, N.310, N.386, T.388 Ligands: NAG-NAG.4 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain C: N.274, N.310, N.386 Ligands: NAG-NAG.3, NAG.20 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: N.241, S.270, N.421 Ligands: NAG-NAG-BMA-MAN-MAN.6 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain G: L.105, N.135, Y.152, T.154, G.298, Q.299 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Y.152 NAG-NAG.9: 6 residues within 4Å: Chain G: T.276, H.308, N.310, N.386, T.388 Ligands: NAG-NAG.10 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain G: N.274, N.310, N.386 Ligands: NAG-NAG.9, NAG.45 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain G: N.241, S.270, S.419, N.421 Ligands: NAG-NAG-BMA-MAN-MAN.12 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 6 residues within 4Å: Chain H: L.105, N.135, Y.152, T.154, G.298, Q.299 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:Y.152 Hydrogen bonds: H:Q.299 NAG-NAG.15: 6 residues within 4Å: Chain H: T.276, H.308, N.310, N.386, T.388 Ligands: NAG-NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain H: N.274, N.310, N.386 Ligands: NAG-NAG.15, NAG.58 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain H: S.270, S.419, N.421 Ligands: NAG-NAG-BMA-MAN-MAN.18 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.6: 10 residues within 4Å: Chain C: E.190, V.233, L.240, N.241, N.354, G.356, C.418, S.419, S.420 Ligands: NAG-NAG.5 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.190, C:G.356, C:S.419 NAG-NAG-BMA-MAN-MAN.12: 11 residues within 4Å: Chain G: E.190, P.191, V.233, L.240, N.241, N.354, G.356, C.418, S.419, S.420 Ligands: NAG-NAG.11 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:G.356, G:S.419 NAG-NAG-BMA-MAN-MAN.18: 11 residues within 4Å: Chain H: E.190, V.233, L.240, N.241, N.354, C.355, G.356, C.418, S.419, S.420 Ligands: NAG-NAG.17 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:E.190, H:S.419

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

NAG.19: 3 residues within 4Å: Chain C: N.280, I.301, Q.415 Ligand excluded by PLIP NAG.20: 8 residues within 4Å: Chain C: E.272, N.274, N.310, I.311, S.312, S.419 Ligands: NAG-NAG.4, NAG-NAG.4 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain C: N.139, K.150 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain C: N.101, D.166, N.168 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain C: R.171, N.176, T.177 Chain G: S.143, H.287 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain C: N.209, T.211, F.212, N.213 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain C: E.248, I.249, N.268, K.322, K.326 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain C: R.313, N.317, W.372, E.376 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain C: V.349, M.350, N.363, T.365 Ligands: NAG.28 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: T.365, N.369 Ligands: NAG.27 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.375 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain D: Q.141, Q.142, N.145 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain D: N.100 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain D: N.110, N.114 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain D: N.105, K.106 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain D: K.122, E.123, S.125, N.126 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain E: Q.141, Q.142, N.145 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain E: N.100, T.102 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain E: N.110, N.114 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain E: N.105 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain E: E.123, N.126 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain F: N.110, N.114 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: K.122, E.123, N.126 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain A: X.109 Chain F: N.100 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain G: N.280, I.301, Q.415 Ligand excluded by PLIP NAG.45: 7 residues within 4Å: Chain G: E.272, N.274, N.310, I.311, S.312 Ligands: NAG-NAG.10, NAG-NAG.10 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain G: S.137, F.138, N.139 Ligands: NAG.47 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain G: N.101 Ligands: NAG.46 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain G: I.163, R.171, N.176, T.177 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain G: N.209, T.211, T.219 Ligands: NAG.55 Ligand excluded by PLIP NAG.50: 6 residues within 4Å: Chain G: E.248, I.249, N.268, E.269, K.322, K.326 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain G: R.313, N.317, W.372, E.376 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain G: V.349, M.350, N.363, T.365 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain G: Q.340, T.365, N.369 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain G: N.375, E.376 Ligand excluded by PLIP NAG.55: 6 residues within 4Å: Chain G: N.213, T.215, S.253, E.254, F.256 Ligands: NAG.49 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain G: N.255, T.257 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain H: N.280, I.301, Q.415 Ligand excluded by PLIP NAG.58: 7 residues within 4Å: Chain H: E.272, N.274, N.310, I.311, S.312 Ligands: NAG-NAG.16, NAG-NAG.16 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain H: S.137, F.138, N.139 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain H: N.101, T.103, N.168 Ligand excluded by PLIP NAG.61: 3 residues within 4Å: Chain C: H.287 Chain H: N.176, T.177 Ligand excluded by PLIP NAG.62: 5 residues within 4Å: Chain H: N.209, T.211, F.212, N.213, T.219 Ligand excluded by PLIP NAG.63: 5 residues within 4Å: Chain H: E.247, E.248, I.249, N.268, K.322 Ligand excluded by PLIP NAG.64: 3 residues within 4Å: Chain H: R.313, N.317, W.372 Ligand excluded by PLIP NAG.65: 5 residues within 4Å: Chain H: V.349, M.350, N.363, T.365 Ligands: NAG.66 Ligand excluded by PLIP NAG.66: 3 residues within 4Å: Chain H: T.365, N.369 Ligands: NAG.65 Ligand excluded by PLIP NAG.67: 2 residues within 4Å: Chain H: N.208, N.220 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

RQk-Base-A pAb heavy chain: A
RQk-Base-A pAb light chain: B
AMC016v4.2 envelope glycoprotein gp120: CGH
AMC016v4.2 transmembrane protein gp41: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

G
E

H
F

D
B

E
C

F
D

RQk-Base-A pAb heavy chain

RQk-Base-A pAb light chain

AMC016v4.2 envelope glycoprotein gp120

AMC016v4.2 transmembrane protein gp41

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