SMTL ID : 5fa2.2 (1 other biounit)

Crystal structure of 426c.TM4deltaV1-3 p120

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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.1: 9 residues within 4Å: Chain A: T.93, D.95, P.96, K.136, L.145, N.146, C.298, K.299, S.300 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.93 Water bridges: A:D.95, A:D.95

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

NAG.2: 2 residues within 4Å: Chain A: N.114, N.124 No protein-ligand interaction detected (PLIP) NAG.3: 3 residues within 4Å: Chain A: T.239, N.253, S.255 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.239, A:T.239, A:N.253, A:S.255 Water bridges: A:S.255 NAG.4: 3 residues within 4Å: Chain A: I.262, S.263, N.264 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.264 NAG.5: 2 residues within 4Å: Chain A: S.202, N.205 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.202 Water bridges: A:S.202 NAG.6: 1 residues within 4Å: Chain A: N.81 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.81 NAG.7: 3 residues within 4Å: Chain A: V.42, N.113, N.125 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.42 Water bridges: A:N.125, A:N.125

2 x FLC: CITRATE ANION(Non-covalent)

FLC.8: 5 residues within 4Å: Chain A: R.195, R.272, K.274, Q.275, I.276 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:R.195 Hydrogen bonds: A:K.274, A:Q.275, A:I.276 Water bridges: A:R.272, A:K.274 Salt bridges: A:R.272, A:K.274 FLC.9: 5 residues within 4Å: Chain A: D.235, L.236, E.237, N.278, K.285 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.235, A:D.235, A:D.235, A:L.236, A:N.278 Water bridges: A:G.234, A:K.274, A:N.278 Salt bridges: A:K.285

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scharf, L. et al., Structural basis for germline antibody recognition of HIV-1 immunogens. Elife (2016)

Release Date

2016-04-06

Peptides

gp120: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

gp120

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