SMTL ID : 9nhi.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.10 Å

Oligo State

hetero-1-1-3-3-mer

Ligands

10 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 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.187 NAG-NAG.2: 6 residues within 4Å: Chain C: T.311, H.343, N.345, N.421, T.423 Ligands: NAG-NAG.3 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain C: N.309, N.345, N.421 Ligands: NAG-NAG.2, NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain C: N.276, S.305, S.454, N.456 Ligands: NAG-NAG-BMA-MAN-MAN.5 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain E: N.276, E.304, N.456 Ligands: NAG-NAG.7, NAG-NAG-BMA-MAN-MAN.9 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 8 residues within 4Å: Chain E: E.307, N.309, N.345, I.346, S.347 Ligands: NAG-NAG.6, NAG-NAG.10, NAG-NAG.10 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain E: T.311, H.343, N.345, N.421, T.423 Ligands: NAG-NAG.10 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain E: N.309, N.345, N.421 Ligands: NAG-NAG.7, NAG-NAG.8 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain G: N.243, K.245, N.255 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain G: L.140, N.170, Y.187, T.189, G.333, Q.334 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Y.187

2 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.5: 9 residues within 4Å: Chain C: E.225, V.268, L.275, N.276, G.391, C.453, S.454, S.455 Ligands: NAG-NAG.4 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.391, C:S.454 NAG-NAG-BMA-MAN-MAN.9: 10 residues within 4Å: Chain E: E.225, P.226, V.268, L.275, N.276, N.389, G.391, S.454, S.455 Ligands: NAG-NAG.6 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.225, E:G.391, E: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.13: 10 residues within 4Å: Chain G: E.225, V.268, L.275, N.276, N.389, G.391, C.453, S.454, S.455 Ligands: NAG.47 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:E.225, G:G.391, G:S.454

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

NAG.14: 3 residues within 4Å: Chain C: E.93, N.94 Chain D: S.17 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain C: N.315, I.336, Q.450 Ligand excluded by PLIP NAG.16: 6 residues within 4Å: Chain C: N.309, N.345, I.346, S.347 Ligands: NAG-NAG.3, NAG-NAG.3 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain C: S.172, F.173, N.174 Ligands: NAG.18 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain C: N.136, T.138, K.185 Ligands: NAG.17 Ligand excluded by PLIP NAG.19: 6 residues within 4Å: Chain C: V.196, R.206, L.207, I.208, C.210, N.211 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain C: N.244, T.246, F.247, N.248, T.254 Ligand excluded by PLIP NAG.21: 7 residues within 4Å: Chain C: E.282, E.283, I.284, N.303, E.304, K.357, K.361 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain C: R.348, N.352, W.407, E.411 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain C: V.384, M.385, N.398, T.400 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain C: Q.375, T.400, N.404 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: Y.408, N.410 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain D: N.100, T.102 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain D: N.105 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain D: K.122, E.123, N.126 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain E: V.91, N.243, N.255 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain E: N.136 Ligand excluded by PLIP NAG.31: 6 residues within 4Å: Chain E: L.140, N.170, Y.187, T.189, G.333, Q.334 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain E: N.174 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain E: N.398, T.400 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain E: R.206, N.211 Chain G: H.322 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain E: N.315, I.336, Q.450 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain E: N.352, W.407 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain E: E.93, N.94 Chain F: G.13, S.17 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain E: N.244, T.246, T.254 Ligands: NAG.39 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain E: N.248, T.250, S.288, E.289 Ligands: NAG.38 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain F: Q.141, Q.142, N.145 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain C: S.178, H.322 Chain G: N.211, T.212 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain G: S.172, F.173, N.174 Ligands: NAG.55 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain G: N.244, T.246, F.247, N.248, T.254 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain G: N.248, T.250, S.288, E.289 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain G: N.290, T.292, D.293 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain G: E.282, I.284, N.303, K.357 Ligand excluded by PLIP NAG.47: 5 residues within 4Å: Chain G: N.276, S.305, S.454, N.456 Ligands: NAG-NAG-BMA.13 Ligand excluded by PLIP NAG.48: 7 residues within 4Å: Chain G: E.307, N.309, N.345, I.346, S.347, S.454 Ligands: NAG.49 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain G: N.345, N.421 Ligands: NAG.48, NAG.50 Ligand excluded by PLIP NAG.50: 6 residues within 4Å: Chain G: T.311, H.343, N.345, N.421, T.423 Ligands: NAG.49 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain G: N.315, I.336, Q.450 Ligand excluded by PLIP NAG.52: 5 residues within 4Å: Chain G: V.384, M.385, N.398, T.400 Ligands: NAG.53 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain G: Q.375, T.400, N.404 Ligands: NAG.52 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain G: Y.408, N.410 Ligand excluded by PLIP NAG.55: 4 residues within 4Å: Chain G: N.136, K.185, N.203 Ligands: NAG.42 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-C pAb heavy chain: A
RQk-Base-C pAb light chain: B
AMC016 v4.2 gp120: CEG
AMC016 v4.2 gp41: DFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

E
C

G
D

D
B

F
E

H
F

RQk-Base-C pAb heavy chain

RQk-Base-C pAb light chain

AMC016 v4.2 gp120

AMC016 v4.2 gp41

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