Research workbench
Crystal structure of runx-1/AML1/CBFALPHA runt domain- cbfbeta core domain heterodimer and C/EBPBETA bzip homodimer bound to a DNA fragment from the csf-1R promoter
Analyse Crystal structure of runx-1/AML1/CBFALPHA runt domain- cbfbeta core domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IO4
- Type
- protein + DNA
- Length
- 433 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Csf-1R promoter; CAAT/ENHANCER binding protein beta; Runt-related transcription factor 1…
- UniProt
- P17676, Q03347, Q08024
- Ligands
- AU
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Csf-1R promoter | dna | 26 | — | — |
| F | Csf-1R promoter | dna | 26 | — | — |
| A | CAAT/ENHANCER binding protein beta | protein | 63 | 92% helix, 0% strand | P17676 |
| B | CAAT/ENHANCER binding protein beta | protein | 70 | 87% helix, 0% strand | P17676 |
| C | Runt-related transcription factor 1 | protein | 120 | 0% helix, 39% strand | Q03347 |
| D | Core-binding factor, beta subunit | protein | 128 | 30% helix, 34% strand | Q08024 |
Ligands and binding sites
- AU · Gold ion · metal · 3 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 541 | 0.67 | 0.78 | 32 | empty |
| 2 | 328 | 0.60 | 0.77 | 22 | empty |
| 3 | 187 | 0.53 | 0.79 | 23 | empty |
| 4 | 225 | 0.49 | 0.75 | 30 | empty |
| 5 | 131 | 0.41 | 0.75 | 17 | AU |
Interfaces
9 interfaces between chains.
- C–D · 1114 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1110 Ų buried · 87 hydrogen bonds · nucleic-nucleic
- A–B · 1004 Ų buried · 2 hydrogen bonds · protein-protein
- F–C · 453 Ų buried · 11 hydrogen bonds · protein-nucleic
- E–C · 423 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 1IO4 · Crystal structure of runx-1/AML1/CBFALPHA runt domain-cbfbeta core domain heterodimer and… · the same entry in another collection · chain D against D, TM-score 1.00
- Q03347 · AlphaFold monomer V2.0 prediction for runt-related transcription factor 1 (Q03347) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q08024 · AlphaFold monomer V2.0 prediction for core-binding factor subunit beta (Q08024) · a predicted model of the same protein · chain D against A, TM-score 0.95
- P17676 · AlphaFold monomer V2.0 prediction for CCAAT/ENHANCER-binding protein beta (P17676) · a predicted model of the same protein · chain B 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 P17676
- Every structure of UniProt Q03347
- Every structure of UniProt Q08024
- Elsewhere: RCSB PDB 1IO4 · PDBe 1IO4 · UniProt P17676 · UniProt Q03347 · UniProt Q08024
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