Research workbench
Crystal structure of runx-1/AML1/CBFALPHA runt domain 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 and C/EBPBETA bzip… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HJB
- Type
- protein + DNA
- Length
- 613 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CCAAT/ENHANCER binding protein beta; Runt-related transcription factor 1; DNA…
- UniProt
- P17676, Q03347
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 58% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CCAAT/ENHANCER binding protein beta | protein | 66 | 92% helix, 0% strand | P17676 |
| B | CCAAT/ENHANCER binding protein beta | protein | 67 | 93% helix, 0% strand | P17676 |
| C, F | Runt-related transcription factor 1 | protein | 120 | 0% helix, 42% strand | Q03347 |
| D, E | CCAAT/ENHANCER binding protein beta | protein | 68 | 91% helix, 0% strand | P17676 |
| G, I | DNA (5'-(*GP*AP*AP*GP*AP*TP*TP*TP*CP*CP* AP*AP*AP*CP*TP*CP*TP*GP*TP*GP*GP*TP*TP*GP*CP*G)-3') | dna | 26 | — | — |
| H, J | DNA (5'-(*CP*CP*GP*CP*AP*AP*CP*CP*AP*CP* AP*GP*AP*GP*TP*TP*TP*GP*GP*AP*AP*AP*TP*CP*TP*T)-3') | dna | 26 | — | — |
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 557 | 0.69 | 0.78 | 35 | empty |
| 2 | 442 | 0.64 | 0.78 | 33 | empty |
| 3 | 211 | 0.55 | 0.79 | 25 | empty |
| 4 | 92 | 0.50 | 0.83 | 16 | empty |
| 5 | 194 | 0.49 | 0.76 | 18 | empty |
Interfaces
19 interfaces between chains.
- I–J · 1116 Ų buried · 94 hydrogen bonds · nucleic-nucleic
- G–H · 1099 Ų buried · 117 hydrogen bonds · nucleic-nucleic
- A–B · 1010 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 977 Ų buried · 4 hydrogen bonds · protein-protein
- F–J · 477 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 1HJB · Crystal structure of runx-1/AML1/CBFALPHA runt domain and C/EBPBETA bzip homodimer bound… · the same entry in another collection · chain J against J, 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
- P17676 · AlphaFold monomer V2.0 prediction for CCAAT/ENHANCER-binding protein beta (P17676) · a predicted model of the same protein · chain A against A, TM-score 0.91
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
- Elsewhere: RCSB PDB 1HJB · PDBe 1HJB · UniProt P17676 · UniProt Q03347
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