MolNFT v1 · #190496 · protein
Cryo-EM structure of the CCL2 bound CCR2-gi complex
7XA3 · Isoform B of C-C chemokine receptor type 2: “Cryo-EM structure of the CCL2 bound CCR2-gi complex”. Electron microscopy, 14 pockets (best druggability 0.83). MolNFT v1 #190496 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7XA3
- Type
- protein
- Length
- 1,220 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform B of C-C chemokine receptor type 2; C-C motif chemokine 2; Guanine…
- UniProt
- P41597, P13500, P63096, P62873, P59768
- Pockets
- 14 · best druggability 0.83
Structure
electron microscopy · 6 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Isoform B of C-C chemokine receptor type 2 | protein | 295 | 81% helix, 4% strand | P41597 |
| L | C-C motif chemokine 2 | protein | 69 | 16% helix, 25% strand | P13500 |
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 229 | 45% helix, 17% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 9% helix, 47% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 58 | 59% helix, 0% strand | P59768 |
| E | SCFV16 | protein | 230 | 4% helix, 47% strand | — |
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.83 | 0.84 | 70 | empty |
| 2 | 234 | 0.80 | 0.93 | 46 | empty |
| 3 | 1003 | 0.77 | 0.79 | 84 | empty |
| 4 | 426 | 0.64 | 0.78 | 48 | empty |
| 5 | 187 | 0.59 | 0.82 | 29 | empty |
Interfaces
7 interfaces between chains.
- B–C · 2149 Ų buried · 10 hydrogen bonds · protein-protein
- R–L · 1399 Ų buried · 15 hydrogen bonds · protein-protein
- R–A · 1274 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1215 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 560 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7XA3 · Cryo-EM structure of the CCL2 bound CCR2-Gi complex · the same entry in another collection · chain E against E, 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 0.99
- P41597 · AlphaFold monomer V2.0 prediction for C-C chemokine receptor type 2 (P41597) · a predicted model of the same protein · chain R against A, TM-score 0.92
- 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 C against A, TM-score 0.92
- P13500 · AlphaFold monomer V2.0 prediction for C-C motif chemokine 2 (P13500) · a predicted model of the same protein · chain L against A, TM-score 0.83
- 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 P41597
- Every structure of UniProt P13500
- Every structure of UniProt P63096
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7XA3 · PDBe 7XA3 · UniProt P41597 · UniProt P13500 · UniProt P63096 · UniProt P62873 · UniProt P59768
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