SMTL ID : 8zpl.1

Cryo-EM strucutre of CXCR4 complexed with antagonist HF51116

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 8 residues within 4Å: Chain B: L.346, G.350, I.353, L.354, I.361, V.388, L.392, F.395 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.346, B:I.353, B:L.354, B:V.388, B:L.392, B:F.395 CLR.2: 5 residues within 4Å: Chain B: L.392, A.393, A.396, C.397, L.436 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.392, B:A.396

1 x 01: (2S)-N-[[4-[[3-(cyclohexylamino)propylamino]methyl]phenyl]methyl]-5-(diaminomethylideneamino)-2-(pyridin-2-ylmethylamino)pentanamide

01.3: 16 residues within 4Å: Chain B: W.232, D.235, W.240, V.250, H.251, C.324, D.325, R.326, Y.328, Q.338, D.408, L.412, H.427, I.430, S.431, E.434 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:W.232, B:W.232, B:W.232, B:W.240, B:V.250, B:Y.328, B:I.430 Hydrogen bonds: B:D.235, B:C.324, B:Q.338, B:D.408, B:H.427, B:E.434 Salt bridges: B:D.408

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
N

B
R

Membrane

We predict this structure to be a membrane protein.
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Nb6 nanobody

Soluble cytochrome b562,C-X-C chemokine receptor type 4

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