MolNFT v1 · #127902 · protein
Co-crystal structure of an MECP2 peptide with TBLR1 WD40 domain
5NAF · F-box-LIKE/WD repeat-containing protein TBL1XR1: “Co-crystal structure of an MECP2 peptide with TBLR1 WD40 domain”. X-ray diffraction, 14 pockets (best druggability 0.81). MolNFT v1 #127902 on GenesisL1: 3D structure, binding sites…
- PDB
- 5NAF
- Type
- protein
- Length
- 1,391 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- F-box-LIKE/WD repeat-containing protein TBL1XR1; Methyl-cpg-binding protein 2
- UniProt
- Q8BHJ5, Q9Z2D6
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 1% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | F-box-LIKE/WD repeat-containing protein TBL1XR1 | protein | 352 | 1% helix, 51% strand | Q8BHJ5 |
| B | F-box-LIKE/WD repeat-containing protein TBL1XR1 | protein | 348 | 1% helix, 51% strand | Q8BHJ5 |
| C | F-box-LIKE/WD repeat-containing protein TBL1XR1 | protein | 339 | 0% helix, 54% strand | Q8BHJ5 |
| D | F-box-LIKE/WD repeat-containing protein TBL1XR1 | protein | 331 | 0% helix, 53% strand | Q8BHJ5 |
| E | Methyl-cpg-binding protein 2 | protein | 11 | 55% helix, 0% strand | Q9Z2D6 |
| F | Methyl-cpg-binding protein 2 | protein | 10 | 30% helix, 0% strand | Q9Z2D6 |
Ligands and binding sites
- GOL · Glycerol · additive · 19 copies · chains A, B, F, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.81 | 0.82 | 65 | GOL |
| 2 | 956 | 0.79 | 0.81 | 64 | GOL |
| 3 | 1088 | 0.73 | 0.76 | 61 | empty |
| 4 | 939 | 0.70 | 0.75 | 56 | GOL |
| 5 | 149 | 0.63 | 0.85 | 28 | empty |
Interfaces
4 interfaces between chains.
- A–E · 560 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 551 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 434 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 15 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 5NAF · Co-crystal structure of an MeCP2 peptide with TBLR1 WD40 domain · the same entry in another collection · chain F against F, TM-score 1.00
- Q8BHJ5 · AlphaFold monomer V2.0 prediction for F-box-LIKE/WD repeat-containing protein TBL1XR1… · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q9Z2D6 · AlphaFold monomer V2.0 prediction for methyl-cpg-binding protein 2 (Q9Z2D6) · a predicted model of the same protein · chain F against A, TM-score 0.44
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 Q8BHJ5
- Every structure of UniProt Q9Z2D6
- Elsewhere: RCSB PDB 5NAF · PDBe 5NAF · UniProt Q8BHJ5 · UniProt Q9Z2D6
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