Research workbench
Crystal structure of MBTD1 YY1 complex
Analyse Crystal structure of MBTD1 YY1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C5I
- Type
- protein
- Length
- 854 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mbt domain-containing protein 1; Transcriptional repressor protein YY1
- UniProt
- Q05BQ5, P25490
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mbt domain-containing protein 1 | protein | 423 | 16% helix, 30% strand | Q05BQ5 |
| B | Mbt domain-containing protein 1 | protein | 415 | 16% helix, 30% strand | Q05BQ5 |
| C | Transcriptional repressor protein YY1 | protein | 16 | 0% helix, 63% strand | P25490 |
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 575 | 0.83 | 0.88 | 59 | empty |
| 2 | 813 | 0.80 | 0.83 | 73 | empty |
| 3 | 851 | 0.80 | 0.82 | 69 | empty |
| 4 | 542 | 0.76 | 0.84 | 37 | empty |
| 5 | 680 | 0.69 | 0.76 | 50 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1202 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 746 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4C5I · Crystal structure of MBTD1 YY1 complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q05BQ5 · AlphaFold monomer V2.0 prediction for mbt domain-containing protein 1 (Q05BQ5) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P25490 · AlphaFold monomer V2.0 prediction for transcriptional repressor protein YY1 (P25490) · a predicted model of the same protein · chain C against A, TM-score 0.36
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 Q05BQ5
- Every structure of UniProt P25490
- Elsewhere: RCSB PDB 4C5I · PDBe 4C5I · UniProt Q05BQ5 · UniProt P25490
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