SMTL ID : 7t73.1

HIV-1 Envelope ApexGT2.2MUT in complex with PCT64.LMCA Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-3-3-mer

Ligands

8 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: 5 residues within 4Å: Chain A: Y.115 Chain C: T.129, Q.131, S.151, N.153 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain C: N.137, N.149, Y.166, G.312, D.313 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.166 NAG-NAG.4: 5 residues within 4Å: Chain C: T.364, T.365, N.378, S.380 Ligands: NAG.19 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: N.255, P.284, N.439 Ligands: NAG-NAG-BMA-MAN.3 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain E: N.137, N.149, Y.166, L.168, D.313 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.166 NAG-NAG.9: 4 residues within 4Å: Chain E: T.364, T.365, N.378, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain F: T.290, H.322, N.324, T.406 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain F: T.364, T.365, N.378, S.380 Ligands: NAG.43 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.3: 9 residues within 4Å: Chain C: P.205, V.247, L.254, N.255, N.369, G.371, V.437, S.438 Ligands: NAG-NAG.5 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.437 NAG-NAG-BMA-MAN.8: 8 residues within 4Å: Chain E: S.202, E.204, V.247, N.255, N.369, V.437, S.438 Ligands: NAG.34 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:V.437 Hydrogen bonds: E:E.204, E:V.437 NAG-NAG-BMA-MAN.11: 9 residues within 4Å: Chain F: P.205, V.247, L.254, N.255, N.369, G.371, V.437, S.438 Ligands: NAG.41 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:V.437 Hydrogen bonds: F:G.371, F:S.202

2 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.6: 8 residues within 4Å: Chain A: D.106, Y.119 Chain B: T.57, G.58 Chain E: T.129, Q.131, N.153, R.162 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.57, B:T.57 NAG-NAG-BMA.10: 7 residues within 4Å: Chain A: T.55 Chain F: V.135, N.137, N.149, Y.166, L.168, D.313 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:Y.166

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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-MAN-MAN.14: 17 residues within 4Å: Chain A: W.33, T.100, G.101, E.103, Y.105, Y.116, F.120 Chain B: S.32, Y.33, Y.50, G.51, S.54, Q.90, Y.92, F.96 Chain F: Q.131, N.153 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.103, A:E.103, B:G.51, A:Y.116, A:Y.116

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

NAG.15: 1 residues within 4Å: Chain C: N.134 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain C: N.294, I.315 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain C: N.269, T.271, N.272 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain C: N.138 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain C: Q.355, S.380, N.384 Ligands: NAG-NAG.4, NAG-NAG.4 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain C: E.88, N.89 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain C: N.288, T.290, H.322, N.324, R.435 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain C: N.347 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain C: Q.286, N.288, N.324, S.326 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain C: R.185, N.190 Chain E: R.301 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.331 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain D: N.126 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain D: N.100, S.102 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain D: N.107, S.109 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain E: N.190 Chain F: R.301 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain E: T.133, N.134, R.144 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain E: N.294, I.315, V.433 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain E: T.290, H.322, N.324, S.404 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain E: Q.286, N.288, N.324, S.326 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain E: N.255, P.284, N.439 Ligands: NAG-NAG-BMA-MAN.8 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain E: N.269, T.271, N.272 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain E: S.380, G.381, N.384 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain E: N.89 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain E: N.331, S.385, W.387 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain F: V.175, R.185, I.187, N.190 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain F: N.294, I.315, V.433 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain F: N.255, P.284, N.439 Ligands: NAG-NAG-BMA-MAN.11 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain F: N.269 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain F: Q.355, S.380, N.384 Ligands: NAG-NAG.13, NAG-NAG.13 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain F: N.89 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain F: N.331, T.386, W.387 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain G: N.100, S.102 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain G: N.107, E.110 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain G: N.126, Y.127 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain H: N.100, S.102, W.103, Y.127 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain H: N.107, E.110 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain H: E.123, N.126 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Willis, J.R. et al., Human immunoglobulin repertoire analysis guides design of vaccine priming immunogens targeting HIV V2-apex broadly neutralizing antibody precursors. Immunity (2022)

Release Date

2022-09-28

Peptides

PCT64.LMCA Fab Heavy Chain: A
PCT64.LMCA Fab Light Chain: B
HIV Envelope ApexGT2.2MUT gp120: CEF
HIV Envelope ApexGT2.2MUT gp41: DGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

E
C

F
E

D
B

G
D

H
F

PCT64.LMCA Fab Heavy Chain

PCT64.LMCA Fab Light Chain

HIV Envelope ApexGT2.2MUT gp120

HIV Envelope ApexGT2.2MUT gp41

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