MolNFT v1 · #175831 · protein
Complex of two rrm domains
7D2Y · Embryonic developmental protein tofu-6: “Complex of two rrm domains”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.65). MolNFT v1 #175831 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7D2Y
- Type
- protein
- Length
- 330 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Embryonic developmental protein tofu-6; RRM2
- UniProt
- Q09293, O76616
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Embryonic developmental protein tofu-6 | protein | 87 | 21% helix, 44% strand | Q09293 |
| B | Embryonic developmental protein tofu-6 | protein | 80 | 23% helix, 38% strand | Q09293 |
| C | RRM2 | protein | 82 | 26% helix, 30% strand | O76616 |
| D | RRM2 | protein | 81 | 22% helix, 31% strand | O76616 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.65 | 0.80 | 36 | empty |
| 2 | 253 | 0.64 | 0.82 | 32 | empty |
| 3 | 63 | 0.30 | 0.74 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–C · 779 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 753 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 589 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 424 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 340 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7D2Y · complex of two RRM domains · the same entry in another collection · chain D against D, TM-score 1.00
- Q09293 · AlphaFold monomer V2.0 prediction for embryonic developmental protein tofu-6 (Q09293) · a predicted model of the same protein · chain B against A, TM-score 0.92
- O76616 · AlphaFold monomer V2.0 prediction for protein pid-3 (O76616) · a predicted model of the same protein · chain D against A, TM-score 0.88
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 Q09293
- Every structure of UniProt O76616
- Elsewhere: RCSB PDB 7D2Y · PDBe 7D2Y · UniProt Q09293 · UniProt O76616
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