MolNFT v1 · #35726 · protein
Crystal structure of RNA-binding motif of human RNA-binding protein 12
2EK1: “Crystal structure of RNA-binding motif of human RNA-binding protein 12”. X-ray diffraction, 6 pockets (best druggability 0.79). MolNFT v1 #35726 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2EK1
- Type
- protein
- Length
- 629 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-binding protein 12
- UniProt
- Q9NTZ6
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, F, H | RNA-binding protein 12 | protein | 79 | 23% helix, 34% strand | Q9NTZ6 |
| B | RNA-binding protein 12 | protein | 78 | 23% helix, 35% strand | Q9NTZ6 |
| D | RNA-binding protein 12 | protein | 79 | 23% helix, 34% strand | Q9NTZ6 |
| G | RNA-binding protein 12 | protein | 77 | 23% helix, 31% strand | Q9NTZ6 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.79 | 0.99 | 30 | empty |
| 2 | 707 | 0.67 | 0.75 | 70 | empty |
| 3 | 219 | 0.48 | 0.75 | 34 | empty |
| 4 | 136 | 0.39 | 0.74 | 26 | empty |
| 5 | 98 | 0.36 | 0.74 | 21 | empty |
Interfaces
13 interfaces between chains.
- G–H · 637 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 609 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 592 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 582 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 454 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified, 4 disulfide (engineered, disulfide).
Compared structures
- 2EK1 · Crystal structure of RNA-binding motif of human rna-binding protein 12 · the same entry in another collection · chain H against H, TM-score 1.00
- Q9NTZ6 · AlphaFold monomer V2.0 prediction for RNA-binding protein 12 (Q9NTZ6) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q9NTZ6
- Elsewhere: RCSB PDB 2EK1 · PDBe 2EK1 · UniProt Q9NTZ6
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