SMTL ID : 5fa2.1 (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- 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.1: 11 residues within 4Å: Chain A: E.19, T.93, D.95, P.96, K.136, L.145, N.146, N.244, C.298, K.299, S.300 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.95, A:D.95, A:T.297

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

NAG.2: 2 residues within 4Å: Chain A: N.114, N.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.114, A:N.124 NAG.3: 3 residues within 4Å: Chain A: K.174, S.202, N.205 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.202, A:N.205 NAG.4: 4 residues within 4Å: Chain A: T.239, T.240, N.253, S.255 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.240 Hydrogen bonds: A:N.253, A:S.255 Water bridges: A:N.253, A:S.255, A:S.255 NAG.5: 2 residues within 4Å: Chain A: R.204, N.264 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.264 NAG.6: 1 residues within 4Å: Chain A: N.81 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.81

2 x FLC: CITRATE ANION(Non-covalent)

FLC.7: 5 residues within 4Å: Chain A: D.235, L.236, E.237, N.278, K.285 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:L.236, A:N.278, A:K.285 Water bridges: A:K.274, A:K.274 Salt bridges: A:K.285, A:K.285 FLC.8: 4 residues within 4Å: Chain A: N.118, L.161, R.162, H.220 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.118 Salt bridges: A:R.162, A:R.162, A:H.220, A:H.220

1 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.9: 4 residues within 4Å: Chain A: V.139, S.242, F.243, F.249 No protein-ligand interaction detected (PLIP)

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
A

gp120

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