SMTL ID : 5uem.1

Crystal structure of 354NC37 Fab in complex with HIV-1 clade AE strain 93TH057 gp120

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 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: N.118, T.120, P.122, S.158, H.220 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.2: 11 residues within 4Å: Chain A: D.95, P.96, K.136, N.146, N.244, R.246, I.300, C.306, V.307, S.308 Ligands: NAG.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.246

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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.3: 7 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, Q.212, E.215, K.216 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.212, A:E.215 Hydrogen bonds: A:Q.212

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

NAG.4: 4 residues within 4Å: Chain A: E.40, H.42, N.113, N.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.113, A:N.125 NAG.5: 8 residues within 4Å: Chain A: N.160, T.162 Chain C: I.2, Y.27, G.28, L.29, D.30, G.94 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.28, C:G.94 NAG.6: 4 residues within 4Å: Chain A: N.179, Y.198, E.200, V.307 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.307 Hydrogen bonds: A:N.179, A:Y.198 NAG.7: 2 residues within 4Å: Chain A: N.253, T.255 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.253 NAG.8: 6 residues within 4Å: Chain A: Q.256, N.259, T.261, C.262, G.270, C.271 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.259, A:T.261, A:G.270, A:G.270 NAG.9: 4 residues within 4Å: Chain A: L.149, S.175, N.309 Ligands: NAG-NAG-BMA-MAN-MAN.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.175, A:S.175

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.10: 5 residues within 4Å: Chain A: R.195, I.281, K.282, Q.283, I.284 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.283, A:I.284 Salt bridges: A:K.282

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Freund, N.T. et al., Coexistence of potent HIV-1 broadly neutralizing antibodies and antibody-sensitive viruses in a viremic controller. Sci Transl Med (2017)

Release Date

2018-01-10

Peptides

clade A/E 93TH057 HIV-1 gp120 core: A
354NC37 Fab Heavy Chain: B
354NC37 Fab Light Chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

clade A/E 93TH057 HIV-1 gp120 core

354NC37 Fab Heavy Chain

354NC37 Fab Light Chain

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