SMTL ID : 8zpm.1

Cryo-EM strucutre of CXCR4 complexed with antagonist AMD070

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x 01: (S)-N1-((1H-Benzo[d]imidazol-2-yl)methyl)-N1-(5,6,7,8-tetrahydroquinolin-8-yl)butane-1,4-diamine

01.1: 11 residues within 4Å: Chain A: Y.183, W.232, D.235, Y.254, C.324, D.325, H.427, I.430, S.431, E.434, F.438 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.232, A:W.232, A:W.232, A:Y.254, A:Y.254, A:I.430 Hydrogen bonds: A:C.324, A:E.434 Salt bridges: A:E.434 pi-Stacking: A:F.438

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 8 residues within 4Å: Chain A: L.346, G.350, I.353, L.354, I.361, V.388, I.391, F.395 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.346, A:I.353, A:L.354, A:I.361, A:V.388, A:I.391, A:F.395, A:F.395 CLR.3: 3 residues within 4Å: Chain A: L.392, A.393, C.397 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sang, X.H. et al., Structural Mechanisms Underlying the Modulation of CXCR4 by Diverse Antagonists. To Be Published

Release Date

2025-02-26

Peptides

Soluble cytochrome b562,C-X-C chemokine receptor type 4: A
Nb6 nanobody: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

B
N

Membrane

We predict this structure to be a membrane protein.
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Soluble cytochrome b562,C-X-C chemokine receptor type 4

Nb6 nanobody

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