Research workbench

Cryo-EM structure of the CCL15(27-92) bound CCR1-Gi complex

Analyse Cryo-EM structure of the CCL15(27-92) bound CCR1-Gi complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7VLA
Type: protein
Length: 1,222 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.7
Source: Homo sapiens
Molecule: Guanine nucleotide-binding protein G(i) subunit alpha-1; Guanine nucleotide-binding…
UniProt: P63096, P62873, P59768, Q16663, P32246
Ligands: CLR
Pockets: 12 · best druggability 0.85

Structure

electron microscopy · resolution 2.7 · 6 distinct chains · 34% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanine nucleotide-binding protein G(i) subunit alpha-1	protein	225	45% helix, 19% strand	P63096
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	339	9% helix, 47% strand	P62873
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	58	60% helix, 0% strand	P59768
L	CCL15(27-92)	protein	64	16% helix, 20% strand	Q16663
R	C-C chemokine receptor type 1	protein	302	78% helix, 4% strand	P32246
S	scFv16	protein	234	4% helix, 47% strand	—

Ligands and binding sites

CLR · Cholesterol · ligand · chains R

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	326	0.85	0.95	41	empty
2	862	0.82	0.85	64	empty
3	850	0.75	0.79	82	empty
4	275	0.59	0.78	42	empty
5	63	0.59	0.90	17	empty

Interfaces

7 interfaces between chains.

B–G · 2162 Å² buried · 13 hydrogen bonds · protein-protein
L–R · 1834 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1200 Å² buried · 17 hydrogen bonds · protein-protein
A–R · 1033 Å² buried · 7 hydrogen bonds · protein-protein
A–S · 561 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

7VLA · Cryo-EM structure of the CCL15(27-92) bound CCR1-gi complex · the same entry in another collection · chain S against S, TM-score 1.00
P62873 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(T)… · a predicted model of the same protein · chain B against A, TM-score 1.00
P59768 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain G against A, TM-score 0.95
P32246 · AlphaFold monomer V2.0 prediction for C-C chemokine receptor type 1 (P32246) · a predicted model of the same protein · chain R against A, TM-score 0.93
Q16663 · AlphaFold monomer V2.0 prediction for C-C motif chemokine 15 (Q16663) · a predicted model of the same protein · chain L against A, TM-score 0.88
P63096 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.82

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P63096
Every structure of UniProt P62873
Every structure of UniProt P59768
Every structure of UniProt Q16663
Every structure of UniProt P32246
Elsewhere: RCSB PDB 7VLA · PDBe 7VLA · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt Q16663 · UniProt P32246

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