SMTL ID : 7n8q.2 (1 other biounit)

Rhesusized RV305 DH677.3 Fab bound to Clade A/E 93TH057 HIV-1 gp120 core.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.120, T.122, P.124, S.160 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.120 NAG.2: 3 residues within 4Å: Chain A: N.115, K.126, N.127 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.115 NAG.3: 7 residues within 4Å: Chain A: P.98, V.140, N.148, N.246, R.248, C.308, S.310 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.140 Hydrogen bonds: A:R.248, A:R.248, A:R.248, A:S.310, A:S.310 NAG.4: 1 residues within 4Å: Chain A: N.162 No protein-ligand interaction detected (PLIP) NAG.5: 6 residues within 4Å: Chain A: E.154, E.155, I.156, N.175, K.176, Q.214 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.176 Hydrogen bonds: A:I.156, A:K.176, A:Q.214 NAG.6: 5 residues within 4Å: Chain A: N.181, T.183, P.185, K.305, N.307 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.181, A:K.305, A:N.307 NAG.7: 2 residues within 4Å: Chain A: E.179, N.204 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.204 NAG.8: 3 residues within 4Å: Chain A: M.242, N.255, T.257 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.255 NAG.9: 4 residues within 4Å: Chain A: N.261, T.263, C.264, C.273 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.261, A:C.264

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tolbert, W.D. et al., Structure and Fc-Effector Function of Rhesusized Variants of Human Anti-HIV-1 IgG1s. Front Immunol (2021)

Release Date

2022-04-06

Peptides

clade A/E 93TH057 HIV-1 gp120 core: A
Rhesusized DH677.3 FAB HEAVY CHAIN: B
Rhesusized DH677.3 FAB LIGHT CHAIN: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

clade A/E 93TH057 HIV-1 gp120 core

Rhesusized DH677.3 FAB HEAVY CHAIN

Rhesusized DH677.3 FAB LIGHT CHAIN

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