MolNFT v1 · #160117 · protein
Cryo-EM structure of urocortin 1-bound corticotropin-releasing factor 2 receptor in complex with gs protein and NB35
6PB1 · Corticotropin-releasing factor receptor 2: “Cryo-EM structure of urocortin 1-bound corticotropin-releasing factor 2 receptor in complex with gs protein…”. Electron microscopy, 2 ligands (PLM, CLR), 13 pockets (best druggability…
- PDB
- 6PB1
- Type
- protein
- Length
- 1,069 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Corticotropin-releasing factor receptor 2; Urocortin; Guanine nucleotide-binding protein…
- UniProt
- Q13324, P55089, P63092, P63096, P62873, P59768
- Ligands
- PLM, CLR
- Pockets
- 13 · best druggability 0.83
Structure
electron microscopy · 6 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | Corticotropin-releasing factor receptor 2 | protein | 281 | 78% helix, 0% strand | Q13324 |
| U | Urocortin | protein | 40 | 78% 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 | 43% helix, 19% strand | P63092, P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 8% helix, 46% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 53% helix, 0% strand | P59768 |
| N | Nanobody 35 | protein | 126 | 5% helix, 44% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.83 | 0.86 | 76 | empty |
| 2 | 973 | 0.76 | 0.79 | 73 | empty |
| 3 | 811 | 0.73 | 0.78 | 71 | empty |
| 4 | 387 | 0.71 | 0.83 | 65 | empty |
| 5 | 212 | 0.56 | 0.79 | 30 | empty |
Interfaces
7 interfaces between chains.
- B–G · 2206 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1574 Ų buried · 18 hydrogen bonds · protein-protein
- P–U · 1505 Ų buried · 9 hydrogen bonds · protein-protein
- P–A · 1096 Ų buried · 10 hydrogen bonds · protein-protein
- A–N · 965 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6PB1 · Cryo-EM structure of Urocortin 1-bound Corticotropin-releasing factor 2 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 1.00
- Q13324 · AlphaFold monomer V2.0 prediction for corticotropin-releasing factor receptor 2 (Q13324) · a predicted model of the same protein · chain P against A, TM-score 0.95
- 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 0.92
- 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
- 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
- P55089 · AlphaFold monomer V2.0 prediction for urocortin (P55089) · a predicted model of the same protein · chain U against A, TM-score 0.70
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 Q13324
- 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 6PB1 · PDBe 6PB1 · UniProt Q13324 · UniProt P55089 · UniProt P63092 · UniProt P63096 · UniProt P62873 · UniProt P59768
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