SMTL ID : 8u4t.1

Structure of tetrameric CXCR4 in complex with REGN7663 Fab

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

16 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 5 residues within 4Å: Chain C: I.261, C.269, F.311 Chain F: F.322 Ligands: CLR.2 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain C Hydrophobic interactions: F:F.322, C:I.261, C:F.311 CLR.2: 7 residues within 4Å: Chain C: F.54, N.55, I.304, L.308 Ligands: CLR.1, D21.4, D21.19 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.54, C:F.54, C:I.304, C:L.308 CLR.3: 5 residues within 4Å: Chain C: L.96, H.97, I.133, Y.175, W.179 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.96, C:I.133, C:Y.175, C:W.179, C:W.179 CLR.5: 6 residues within 4Å: Chain C: T.69, G.73, L.76, P.317, Y.320 Chain L: L.264 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain L Hydrophobic interactions: C:L.76, C:L.76, C:Y.320, L:L.264 CLR.6: 5 residues within 4Å: Chain F: I.261, C.269, F.311 Chain I: F.322 Ligands: CLR.7 3 PLIP interactions: 1 interactions with chain I, 2 interactions with chain F Hydrophobic interactions: I:F.322, F:I.261, F:F.311 CLR.7: 7 residues within 4Å: Chain F: F.54, N.55, I.304, L.308 Ligands: D21.4, CLR.6, D21.9 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:F.54, F:F.54, F:I.304, F:L.308 CLR.8: 5 residues within 4Å: Chain F: L.96, H.97, I.133, Y.175, W.179 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:L.96, F:I.133, F:Y.175, F:W.179, F:W.179 CLR.10: 6 residues within 4Å: Chain C: L.264 Chain F: T.69, G.73, L.76, P.317, Y.320 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain C Hydrophobic interactions: F:L.76, F:L.76, F:Y.320, C:L.264 CLR.11: 5 residues within 4Å: Chain I: I.261, C.269, F.311 Chain L: F.322 Ligands: CLR.12 3 PLIP interactions: 1 interactions with chain L, 2 interactions with chain I Hydrophobic interactions: L:F.322, I:I.261, I:F.311 CLR.12: 7 residues within 4Å: Chain I: F.54, N.55, I.304, L.308 Ligands: D21.9, CLR.11, D21.14 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:F.54, I:F.54, I:I.304, I:L.308 CLR.13: 5 residues within 4Å: Chain I: L.96, H.97, I.133, Y.175, W.179 5 PLIP interactions: 5 interactions with chain I Hydrophobic interactions: I:L.96, I:I.133, I:Y.175, I:W.179, I:W.179 CLR.15: 6 residues within 4Å: Chain F: L.264 Chain I: T.69, G.73, L.76, P.317, Y.320 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain F Hydrophobic interactions: I:L.76, I:L.76, I:Y.320, F:L.264 CLR.16: 5 residues within 4Å: Chain C: F.322 Chain L: I.261, C.269, F.311 Ligands: CLR.17 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain C Hydrophobic interactions: L:I.261, L:F.311, C:F.322 CLR.17: 7 residues within 4Å: Chain L: F.54, N.55, I.304, L.308 Ligands: D21.14, CLR.16, D21.19 4 PLIP interactions: 4 interactions with chain L Hydrophobic interactions: L:F.54, L:F.54, L:I.304, L:L.308 CLR.18: 5 residues within 4Å: Chain L: L.96, H.97, I.133, Y.175, W.179 5 PLIP interactions: 5 interactions with chain L Hydrophobic interactions: L:L.96, L:I.133, L:Y.175, L:W.179, L:W.179 CLR.20: 6 residues within 4Å: Chain I: L.264 Chain L: T.69, G.73, L.76, P.317, Y.320 4 PLIP interactions: 1 interactions with chain I, 3 interactions with chain L Hydrophobic interactions: I:L.264, L:L.76, L:L.76, L:Y.320

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

D21.4: 7 residues within 4Å: Chain C: T.297, K.300, W.301 Chain F: F.54, I.62 Ligands: CLR.2, CLR.7 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:K.300, C:W.301, F:I.62 D21.9: 7 residues within 4Å: Chain F: T.297, K.300, W.301 Chain I: F.54, I.62 Ligands: CLR.7, CLR.12 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain I Hydrophobic interactions: F:K.300, F:W.301, I:I.62 D21.14: 7 residues within 4Å: Chain I: T.297, K.300, W.301 Chain L: F.54, I.62 Ligands: CLR.12, CLR.17 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain L Hydrophobic interactions: I:K.300, I:W.301, L:I.62 D21.19: 7 residues within 4Å: Chain C: F.54, I.62 Chain L: T.297, K.300, W.301 Ligands: CLR.2, CLR.17 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain L Hydrophobic interactions: C:I.62, L:K.300, L:W.301

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: ADGJ
REGN7663 Fab heavy chain: BEHK
C-X-C chemokine receptor type 4: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

D
F

G
O

J
Y

B
H

E
G

H
P

K
Z

C
R

F
I

I
Q

L
AA

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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