Research workbench
Cryo-EM structure of the apo CCR1-gi complex
Analyse Cryo-EM structure of the apo 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
- 7VL8
- Type
- protein
- Length
- 1,132 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(I) subunit alpha-1; Guanine nucleotide-binding…
- UniProt
- P63096, P62873, P59768, P32246
- Ligands
- CLR
- Pockets
- 9 · best druggability 0.82
Structure
electron microscopy · 5 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 | 218 | 45% helix, 19% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 8% helix, 44% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 58 | 55% helix, 0% strand | P59768 |
| R | C-C chemokine receptor type 1 | protein | 284 | 79% helix, 4% strand | P32246 |
| S | SCFV16 | protein | 233 | 1% helix, 46% 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
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 831 | 0.82 | 0.84 | 65 | empty |
| 2 | 757 | 0.72 | 0.78 | 76 | empty |
| 3 | 564 | 0.71 | 0.79 | 36 | empty |
| 4 | 52 | 0.69 | 0.97 | 19 | empty |
| 5 | 361 | 0.64 | 0.79 | 58 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2199 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1139 Ų buried · 11 hydrogen bonds · protein-protein
- A–R · 1076 Ų buried · 9 hydrogen bonds · protein-protein
- A–S · 594 Ų buried · 7 hydrogen bonds · protein-protein
- B–S · 347 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7VL8 · Cryo-EM structure of the Apo 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
- 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 P32246
- Elsewhere: RCSB PDB 7VL8 · PDBe 7VL8 · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P32246
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