SMTL ID : 6ieq.1 (1 other biounit)

Crystal Structure of HIV-1 Env ConM SOSIP.v7 in Complex with bNAb PGT124 and 35O22

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.90 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-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.1: 2 residues within 4Å: Chain A: E.92, N.93 No protein-ligand interaction detected (PLIP)

1 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.2: 6 residues within 4Å: Chain A: N.97, N.231, T.233, G.234, S.271, I.274 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.3: 3 residues within 4Å: Chain A: E.88, N.226, N.238 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain A: N.298, I.321 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain A: R.333, N.390 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.333, A:R.333

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.4: 11 residues within 4Å: Chain A: E.69, S.206, N.259, N.375, G.377, E.426, C.431, T.432, S.433 Ligands: MAN-MAN.5, NAG.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.377 NAG-NAG-BMA-MAN-MAN.6: 8 residues within 4Å: Chain A: E.290, N.292, N.330, I.331, S.332, T.399, R.430 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.10 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.8: 1 residues within 4Å: Chain A: N.384 No protein-ligand interaction detected (PLIP)

1 x MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose(Non-covalent)

MAN-MAN.5: 3 residues within 4Å: Chain A: T.68 Ligands: NAG-NAG-BMA-MAN-MAN.4, NAG-NAG-BMA-MAN-MAN.4 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-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-MAN-MAN-MAN.10: 22 residues within 4Å: Chain A: N.292, R.325, H.328, N.330, T.399, T.401 Chain B: S.25, R.26, N.45, Q.47, P.61, D.62, I.63 Chain C: R.103, I.104, Y.105, G.106, V.107, V.108 Ligands: NAG-NAG-BMA-MAN-MAN.6, MAN.16, MAN.17 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:V.108 Hydrogen bonds: C:V.108, A:R.325

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.11: 1 residues within 4Å: Chain A: N.135 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain A: N.135, N.157, K.168 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.135 Hydrogen bonds: A:K.168, A:K.168 NAG.13: 4 residues within 4Å: Chain A: R.189, I.191, N.194, T.195 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.189, A:N.194, A:N.194 NAG.14: 3 residues within 4Å: Chain A: N.273, T.275, N.276 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.273 NAG.15: 2 residues within 4Å: Chain A: N.434 Ligands: NAG-NAG-BMA-MAN-MAN.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.434

2 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.16: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.10, MAN.17 No protein-ligand interaction detected (PLIP) MAN.17: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.10, MAN.16 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sliepen, K. et al., Structure and immunogenicity of a stabilized HIV-1 envelope trimer based on a group-M consensus sequence. Nat Commun (2019)

Release Date

2019-05-22

Peptides

Envelope glycoprotein gp160: A
PGT124 Fab Light Chain: B
PGT124 Fab Heavy Chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
L

C
H

Envelope glycoprotein gp160

PGT124 Fab Light Chain

PGT124 Fab Heavy Chain

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