SMTL ID : 9nhj.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.04 Å

Oligo State

hetero-1-1-3-3-mer

Ligands

7 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain C: L.140, N.170, Y.187, T.189, G.333, Q.334 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.187 Hydrogen bonds: C:Q.334 NAG-NAG.4: 6 residues within 4Å: Chain E: L.140, N.170, Y.187, T.189, G.333, Q.334 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.187 NAG-NAG.5: 7 residues within 4Å: Chain E: T.311, H.343, N.345, N.421, T.423, R.452 Ligands: NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain E: N.309, N.345, N.421 Ligands: NAG-NAG.5, NAG.22 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain E: S.305, S.454, N.456 Ligands: NAG-NAG-BMA-MAN-MAN.8 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain F: V.91, N.243, N.255, V.256, S.257 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain F: L.140, N.170, Y.187, T.189, G.333, Q.334 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:Y.187

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.2: 8 residues within 4Å: Chain C: S.223, E.225, P.226, L.275, N.276, N.389, S.454, S.455 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.8: 11 residues within 4Å: Chain E: E.225, P.226, V.268, L.275, N.276, N.389, C.390, G.391, S.454, S.455 Ligands: NAG-NAG.7 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.391, E:S.454 NAG-NAG-BMA-MAN-MAN.11: 9 residues within 4Å: Chain F: E.225, V.268, L.275, N.276, N.389, G.391, S.454, S.455 Ligands: NAG.40 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.454

1 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.3: 6 residues within 4Å: Chain A: X.103, X.104, X.105 Chain E: E.93, N.94 Chain G: S.17 No protein-ligand interaction detected (PLIP)

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

NAG.12: 2 residues within 4Å: Chain C: N.315, Q.450 Ligand excluded by PLIP NAG.13: 5 residues within 4Å: Chain C: E.307, N.309, N.345, S.347 Ligands: NAG.14 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain C: N.345, N.421 Ligands: NAG.13 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain C: S.305, S.454, S.455, N.456 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain C: S.172, F.173, N.174 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain C: N.136, T.138, N.203 Ligand excluded by PLIP NAG.18: 6 residues within 4Å: Chain C: V.196, P.197, I.198, R.206, L.207, N.211 Ligand excluded by PLIP NAG.19: 6 residues within 4Å: Chain C: G.378, G.379, V.384, M.385, N.398, T.400 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain C: N.243, N.255 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain E: N.315, I.336, Q.450 Ligand excluded by PLIP NAG.22: 7 residues within 4Å: Chain E: E.307, N.309, N.345, I.346, S.347 Ligands: NAG-NAG.6, NAG-NAG.6 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain E: S.172, F.173, N.174, K.185 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain E: N.136 Ligand excluded by PLIP NAG.25: 6 residues within 4Å: Chain E: V.196, R.206, L.207, N.209, N.211, T.212 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain E: N.244, T.246, T.254, N.255 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain E: E.283, N.303, K.357 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain E: N.352, S.405, W.407 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain E: V.384, M.385, N.398, T.400 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain E: T.400, N.404 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain E: N.410, E.411 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain E: N.290, T.292, D.293 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain E: N.248, T.250, S.288, E.289 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain F: N.211, T.212 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain F: T.134, S.172, N.174 Ligand excluded by PLIP NAG.36: 6 residues within 4Å: Chain F: N.244, T.246, F.247, N.248, T.254 Ligands: NAG.37 Ligand excluded by PLIP NAG.37: 6 residues within 4Å: Chain F: N.248, T.250, S.288, E.289, F.291 Ligands: NAG.36 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain F: N.290, T.292, D.293 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain F: E.282, I.284, N.303, K.357 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain F: S.305, S.454, N.456 Ligands: NAG-NAG-BMA-MAN-MAN.11 Ligand excluded by PLIP NAG.41: 7 residues within 4Å: Chain F: E.307, N.309, N.345, I.346, S.347, S.454 Ligands: NAG.42 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain F: N.345, N.421 Ligands: NAG.41, NAG.43 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain F: H.343, N.345, N.421, T.423 Ligands: NAG.42 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain F: N.315, I.336, Q.450 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain F: V.384, M.385, N.398, T.400 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain F: T.400, Q.401, N.404 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain F: Y.408, N.410 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain F: E.93, N.94 Chain H: G.13, S.17 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain G: Q.141, N.145 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain G: N.100, T.102 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain G: N.110, N.114 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain G: N.105 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain G: K.122, E.123, N.126 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain H: K.122, E.123, N.126 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain H: Q.141, N.145 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-FP-A pAb heavy chain: A
RQk-FP-A pAb light chain: B
AMC016 v4.2 envelope glycoprotein gp120: CEF
AMC016 v4.2 transmembrane protein gp41: DGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

E
C

F
D

D
G

G
E

H
F

RQk-FP-A pAb heavy chain

RQk-FP-A pAb light chain

AMC016 v4.2 envelope glycoprotein gp120

AMC016 v4.2 transmembrane protein gp41

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