Research workbench
Receptor-growth factor crystal structure at 2.20 ångström resolution
Analyse Receptor-growth factor crystal structure at 2.20 ångström resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VZ4
- Type
- protein
- Length
- 298 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GROWTH/DIFFERENTIATION factor 15; Gdnf family receptor alpha-like
- UniProt
- Q99988, Q6UXV0
- Ligands
- BR, SO4
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GROWTH/DIFFERENTIATION factor 15 | protein | 108 | 15% helix, 48% strand | Q99988 |
| B | Gdnf family receptor alpha-like | protein | 190 | 62% helix, 2% strand | Q6UXV0 |
Ligands and binding sites
- BR · Bromide ion · ion · 2 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 219 | 0.66 | 0.84 | 25 | SO4 |
| 2 | 84 | 0.43 | 0.80 | 16 | empty |
| 3 | 104 | 0.40 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 653 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 5VZ4 · Receptor-growth factor crystal structure at 2.20 Angstrom resolution · the same entry in another collection · chain A against A, TM-score 1.00
- Q6UXV0 · AlphaFold monomer V2.0 prediction for gdnf family receptor alpha-like (Q6UXV0) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q99988 · AlphaFold monomer V2.0 prediction for GROWTH/DIFFERENTIATION factor 15 (Q99988) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q99988
- Every structure of UniProt Q6UXV0
- Elsewhere: RCSB PDB 5VZ4 · PDBe 5VZ4 · UniProt Q99988 · UniProt Q6UXV0
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