SMTL ID : 7sk7.1

Cryo-EM structure of human ACKR3 in complex with CXCL12, a small molecule partial agonist CCX662, and an extracellular Fab

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-mer

Ligands

1 x GJ9: (1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium(Non-covalent)

GJ9.1: 19 residues within 4Å: Chain A: Y.53, W.102, S.105, L.106, N.110, H.123, F.126, S.127, L.130, F.131, I.134, S.218, G.222, W.267, Y.270, H.271, Q.303, S.306, L.307 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.53, A:W.102, A:W.102, A:L.130, A:I.134, A:Q.303, A:Q.303, A:L.307 Hydrogen bonds: A:S.105, A:H.271

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 12 residues within 4Å: Chain A: L.86, N.87, I.90, W.94, V.121, L.124, I.125, I.128, N.129, R.164, W.171, F.175 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.90, A:I.90, A:L.124, A:I.125, A:I.128, A:W.171 Hydrogen bonds: A:N.87, A:R.164, A:R.164

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yen, Y.C. et al., Structures of atypical chemokine receptor 3 reveal the basis for its promiscuity and signaling bias. Sci Adv (2022)

Release Date

2022-07-27

Peptides

Atypical chemokine receptor 3: A
Stromal cell-derived factor 1: B
CID25 Fab light chain: C
CID25 Fab heavy chain: D
Anti-Fab nanobody: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
K

Membrane

We predict this structure to be a membrane protein.
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Atypical chemokine receptor 3

Stromal cell-derived factor 1

CID25 Fab light chain

CID25 Fab heavy chain

Anti-Fab nanobody

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