Research workbench
Cryo-EM structure of urocortin 1-bound corticotropin-releasing factor 1 receptor in complex with gs protein and NB35
Analyse Cryo-EM structure of urocortin 1-bound corticotropin-releasing factor 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PB0
- Type
- protein
- Length
- 1,068 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Corticotropin-releasing factor receptor 1; Urocortin; Guanine nucleotide-binding protein…
- UniProt
- P34998, P55089, P63092, P63096, P62873, P59768
- Ligands
- PLM, CLR
- Pockets
- 14 · best druggability 0.83
Structure
electron microscopy · 6 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Corticotropin-releasing factor receptor 1 | protein | 281 | 78% helix, 0% strand | P34998 |
| U | Urocortin | protein | 39 | 79% helix, 0% strand | P55089 |
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms SHORT,GUANINE nucleotide-binding protein G(I) subunit alpha- 1,GUANINE nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 227 | 42% helix, 16% strand | P63092, P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 7% helix, 44% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 51% helix, 0% strand | P59768 |
| N | Nanobody 35 | protein | 126 | 5% helix, 41% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 901 | 0.83 | 0.85 | 83 | empty |
| 2 | 1008 | 0.76 | 0.79 | 73 | empty |
| 3 | 1097 | 0.76 | 0.78 | 76 | empty |
| 4 | 272 | 0.69 | 0.85 | 51 | empty |
| 5 | 332 | 0.64 | 0.80 | 35 | empty |
Interfaces
7 interfaces between chains.
- B–G · 2220 Ų buried · 14 hydrogen bonds · protein-protein
- R–U · 1540 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1528 Ų buried · 16 hydrogen bonds · protein-protein
- R–A · 1110 Ų buried · 8 hydrogen bonds · protein-protein
- A–N · 953 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6PB0 · Cryo-EM structure of Urocortin 1-bound Corticotropin-releasing factor 1 receptor in… · the same entry in another collection · chain N against N, 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
- P34998 · AlphaFold monomer V2.0 prediction for corticotropin-releasing factor receptor 1 (P34998) · a predicted model of the same protein · chain R against A, TM-score 0.94
- 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 0.88
- P63092 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(S) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.84
- P55089 · AlphaFold monomer V2.0 prediction for urocortin (P55089) · a predicted model of the same protein · chain U 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 0.74
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 P34998
- Every structure of UniProt P55089
- Every structure of UniProt P63092
- Every structure of UniProt P63096
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 6PB0 · PDBe 6PB0 · UniProt P34998 · UniProt P55089 · UniProt P63092 · UniProt P63096 · UniProt P62873 · UniProt P59768
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