MolNFT v1 · #161062 · protein
Cryo-EM structure of extracellular dimeric complex of RET/GFRAL/GDF15
6Q2J · GROWTH/DIFFERENTIATION factor 15: “Cryo-EM structure of extracellular dimeric complex of RET/GFRAL/GDF15”. Electron microscopy, 2 ligands (NAG, CA), 20 pockets (best druggability 0.78). MolNFT v1 #161062 on GenesisL1: 3D structure…
- PDB
- 6Q2J
- Type
- protein
- Length
- 1,738 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GROWTH/DIFFERENTIATION factor 15; Gdnf family receptor alpha-like; Proto-oncogene…
- EC
- 2.7.10.1
- UniProt
- Q99988, Q6UXV0, P07949
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 3 distinct chains · 19% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | GROWTH/DIFFERENTIATION factor 15 | protein | 108 | 15% helix, 48% strand | Q99988 |
| C, D | Gdnf family receptor alpha-like | protein | 190 | 60% helix, 1% strand | Q6UXV0 |
| E, F | Proto-oncogene tyrosine-protein kinase receptor ret (EC 2.7.10.1) | protein | 571 | 7% helix, 40% strand | P07949 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains E, C, F, D
- CA · Calcium ion · metal · 8 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.78 | 0.87 | 56 | empty |
| 2 | 346 | 0.76 | 0.86 | 49 | empty |
| 3 | 437 | 0.69 | 0.81 | 51 | empty |
| 4 | 204 | 0.67 | 0.85 | 23 | empty |
| 5 | 249 | 0.64 | 0.82 | 31 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1439 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 1259 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 1253 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 592 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 588 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 55 disulfide, 14 glycan (disulfide, N-glycosylation).
Compared structures
- 6Q2J · Cryo-EM structure of extracellular dimeric complex of RET/GFRAL/GDF15 · the same entry in another collection · chain F against F, TM-score 1.00
- P07949 · AlphaFold monomer V2.0 prediction for proto-oncogene tyrosine-protein kinase receptor ret… · a predicted model of the same protein · chain E against A, TM-score 0.98
- Q6UXV0 · AlphaFold monomer V2.0 prediction for gdnf family receptor alpha-like (Q6UXV0) · a predicted model of the same protein · chain C 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 B against A, TM-score 0.93
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
- Every structure of UniProt P07949
- Elsewhere: RCSB PDB 6Q2J · PDBe 6Q2J · UniProt Q99988 · UniProt Q6UXV0 · UniProt P07949
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.