MolNFT v1 · #159238 · protein
Cryoem structure of arabidopsis dr complex (DMS3-RDM1)
6OIS · Protein RDM1: “Cryoem structure of arabidopsis dr complex (DMS3-RDM1)”. Electron microscopy, 20 pockets (best druggability 0.83). MolNFT v1 #159238 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6OIS
- Type
- protein
- Length
- 1,365 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein RDM1; Protein defective in meristem silencing 3
- UniProt
- Q9LUJ3, Q94A79
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 49% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein RDM1 | protein | 123 | 59% helix, 1% strand | Q9LUJ3 |
| B | Protein RDM1 | protein | 125 | 61% helix, 1% strand | Q9LUJ3 |
| C | Protein defective in meristem silencing 3 | protein | 330 | 51% helix, 11% strand | Q94A79 |
| D, F | Protein defective in meristem silencing 3 | protein | 229 | 32% helix, 17% strand | Q94A79 |
| E | Protein defective in meristem silencing 3 | protein | 329 | 52% helix, 12% strand | Q94A79 |
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.83 | 0.84 | 94 | empty |
| 2 | 999 | 0.83 | 0.84 | 76 | empty |
| 3 | 497 | 0.69 | 0.79 | 53 | empty |
| 4 | 377 | 0.65 | 0.79 | 47 | empty |
| 5 | 52 | 0.54 | 0.89 | 21 | empty |
Interfaces
10 interfaces between chains.
- C–D · 1829 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 1828 Ų buried · 39 hydrogen bonds · protein-protein
- B–E · 1491 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 1454 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1261 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6OIS · CryoEM structure of Arabidopsis DR complex (DMS3-RDM1) · the same entry in another collection · chain F against F, TM-score 1.00
- Q94A79 · AlphaFold monomer V2.0 prediction for protein defective in meristem silencing 3 (Q94A79) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q9LUJ3 · AlphaFold monomer V2.0 prediction for protein RDM1 (Q9LUJ3) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q9LUJ3
- Every structure of UniProt Q94A79
- Elsewhere: RCSB PDB 6OIS · PDBe 6OIS · UniProt Q9LUJ3 · UniProt Q94A79
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