SMTL ID : 8u4s.1

Structure of trimeric CXCR4 in complex with REGN7663 Fab

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

6 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 9 residues within 4Å: Chain C: L.96, H.97, V.100, L.104, V.132, I.133, V.136, Y.175, W.179 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.96, C:V.100, C:L.104, C:V.132, C:I.133, C:V.136, C:Y.175 CLR.3: 12 residues within 4Å: Chain C: I.261, L.264, C.269, L.315 Chain F: I.261, L.315, I.318, L.319 Ligands: D21.2, D21.5, CLR.6, CLR.9 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain C Hydrophobic interactions: F:L.315, F:I.318, F:L.319, C:I.261, C:L.264, C:L.315 CLR.4: 9 residues within 4Å: Chain F: L.96, H.97, V.100, L.104, V.132, I.133, V.136, Y.175, W.179 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:L.96, F:V.100, F:L.104, F:V.132, F:I.133, F:V.136, F:Y.175 CLR.6: 12 residues within 4Å: Chain F: I.261, L.264, C.269, L.315 Chain I: I.261, L.315, I.318, L.319 Ligands: CLR.3, D21.5, D21.8, CLR.9 6 PLIP interactions: 3 interactions with chain I, 3 interactions with chain F Hydrophobic interactions: I:L.315, I:I.318, I:L.319, F:I.261, F:L.264, F:L.315 CLR.7: 9 residues within 4Å: Chain I: L.96, H.97, V.100, L.104, V.132, I.133, V.136, Y.175, W.179 7 PLIP interactions: 7 interactions with chain I Hydrophobic interactions: I:L.96, I:V.100, I:L.104, I:V.132, I:I.133, I:V.136, I:Y.175 CLR.9: 12 residues within 4Å: Chain C: I.261, L.315, I.318, L.319 Chain I: I.261, L.264, C.269, L.315 Ligands: D21.2, CLR.3, CLR.6, D21.8 6 PLIP interactions: 3 interactions with chain I, 3 interactions with chain C Hydrophobic interactions: I:I.261, I:L.264, I:L.315, C:L.315, C:I.318, C:L.319

3 x D21: (2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate(Non-covalent)

D21.2: 13 residues within 4Å: Chain C: N.51, F.54, I.62, L.308, F.311 Chain I: T.297, K.300, W.301, I.304 Ligands: CLR.3, D21.5, D21.8, CLR.9 12 PLIP interactions: 6 interactions with chain I, 6 interactions with chain C Hydrophobic interactions: I:W.301, I:W.301, I:I.304, C:F.54, C:I.62, C:L.308, C:F.311 Hydrogen bonds: I:T.297, I:T.297, C:N.51, C:F.54 Salt bridges: I:K.300 D21.5: 13 residues within 4Å: Chain C: T.297, K.300, W.301, I.304 Chain F: N.51, F.54, I.62, L.308, F.311 Ligands: D21.2, CLR.3, CLR.6, D21.8 12 PLIP interactions: 6 interactions with chain F, 6 interactions with chain C Hydrophobic interactions: F:F.54, F:I.62, F:L.308, F:F.311, C:W.301, C:W.301, C:I.304 Hydrogen bonds: F:N.51, F:F.54, C:T.297, C:T.297 Salt bridges: C:K.300 D21.8: 13 residues within 4Å: Chain F: T.297, K.300, W.301, I.304 Chain I: N.51, F.54, I.62, L.308, F.311 Ligands: D21.2, D21.5, CLR.6, CLR.9 12 PLIP interactions: 6 interactions with chain F, 6 interactions with chain I Hydrophobic interactions: F:W.301, F:W.301, F:I.304, I:F.54, I:I.62, I:L.308, I:F.311 Hydrogen bonds: F:T.297, F:T.297, I:N.51, I:F.54 Salt bridges: F:K.300

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saotome, K. et al., Structural insights into CXCR4 modulation and oligomerization. Biorxiv (2024)

Release Date

2024-03-13

Peptides

REGN7663 Fab light chain: ADG
REGN7663 Fab heavy chain: BEH
C-X-C chemokine receptor type 4: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

D
A

G
E

B
H

E
B

H
F

C
R

F
C

I
G

Membrane

We predict this structure to be a membrane protein.
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REGN7663 Fab light chain

REGN7663 Fab heavy chain

C-X-C chemokine receptor type 4

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