SMTL ID : 6uda.1

Cryo-EM structure of CH235UCA bound to Man5-enriched CH505.N279K.G458Y.SOSIP.664

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

3 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: 6 residues within 4Å: Chain A: D.196, L.246, N.247, I.429, S.430 Ligands: NAG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.196 NAG-NAG-BMA-MAN.2: 6 residues within 4Å: Chain E: D.196, L.246, N.247, I.429, S.430 Ligands: NAG.6 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.196 NAG-NAG-BMA-MAN.3: 6 residues within 4Å: Chain I: D.196, L.246, N.247, I.429, S.430 Ligands: NAG.8 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:D.196

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

NAG.4: 3 residues within 4Å: Chain A: S.276, N.431 Ligands: NAG-NAG-BMA-MAN.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.276, A:N.431 NAG.5: 1 residues within 4Å: Chain A: N.261 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain E: S.276, N.431 Ligands: NAG-NAG-BMA-MAN.2 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.276, E:N.431 NAG.7: 1 residues within 4Å: Chain E: N.261 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain I: S.276, N.431 Ligands: NAG-NAG-BMA-MAN.3 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:S.276, I:N.431 NAG.9: 1 residues within 4Å: Chain I: N.261 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

LaBranche, C.C. et al., Neutralization-guided design of HIV-1 envelope trimers with high affinity for the unmutated common ancester of CH235 lineage CD4bs broadly neutralizing antibodies. Plos Pathog. (2019)

Release Date

2019-10-02

Peptides

CH505.N279K.G458Y.SOSIP.664 gp120: AEI
CH235 UCA heavy chain Fab: BGK
CH505.N279K.G458Y.SOSIP.664 gp41: CFJ
CH235 UCA light chain Fab: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

I
I

B
C

G
G

K
K

C
Z

F
F

J
J

D
D

H
H

L
L

CH505.N279K.G458Y.SOSIP.664 gp120

CH235 UCA heavy chain Fab

CH505.N279K.G458Y.SOSIP.664 gp41

CH235 UCA light chain Fab

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