SMTL ID : 5cez.1 (1 other biounit)

Crystal Structure of the BG505 SOSIP gp140 HIV-1 Env trimer in Complex with an early putative precursor of the PGT121 family at 3.0 Angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.03 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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-MAN-MAN.1: 13 residues within 4Å: Chain A: T.32, E.33, S.178, P.181, V.223, N.231, N.345, C.346, G.347, C.412, V.413, S.414 Ligands: NAG-NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.347

6 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: 3 residues within 4Å: Chain A: P.260, N.415 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.1 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: Q.262, N.264, N.300, V.301, S.302, R.411 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.354, S.356 Ligands: NAG.14 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: N.203, T.205, P.207, S.243, I.246 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: R.161, I.163, N.166 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain A: T.101, N.102 No protein-ligand interaction detected (PLIP)

1 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.8: 4 residues within 4Å: Chain A: V.103, N.117, S.119, Y.134 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.9: 3 residues within 4Å: Chain A: N.270, I.291, V.409 No protein-ligand interaction detected (PLIP)

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.10: 2 residues within 4Å: Chain A: E.56, N.57 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-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-MAN.11: 19 residues within 4Å: Chain A: R.295, H.298, N.300, S.380, T.382, R.411 Chain B: S.29, N.49, Q.51, P.65, D.66, I.67 Chain C: K.102, R.103, I.104, G.106, M.107, V.108 Ligands: MAN.15 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:K.102, C:V.108, A:R.295, A:R.295

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

NAG.12: 4 residues within 4Å: Chain A: T.97, Q.99, S.119, N.121 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.99 Hydrogen bonds: A:N.121 NAG.13: 3 residues within 4Å: Chain A: N.245, T.247, N.248 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.245, A:T.247 NAG.14: 6 residues within 4Å: Chain A: N.331, S.332, T.340, N.354, S.356 Ligands: NAG-NAG.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.331, A:S.356

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

MAN.15: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.11, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garces, F. et al., Affinity Maturation of a Potent Family of HIV Antibodies Is Primarily Focused on Accommodating or Avoiding Glycans. Immunity (2015)

Release Date

2015-12-23

Peptides

Envelope glycoprotein gp160: A
3H+109L Fab Light Chain: B
3H+109L Fab Heavy Chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
L

C
H

Envelope glycoprotein gp160

3H+109L Fab Light Chain

3H+109L Fab Heavy Chain

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