Research workbench
Crystal structure of the DNA binding domains of human transcription factor ERG, human Runx2 bound to core binding factor beta (Cbfb), and mithramycin, in complex with 16mer DNA CAGAGGATGTGGCTTC
Analyse Crystal structure of the DNA binding domains of human transcription factor ERG… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VGG
- Type
- protein + DNA
- Length
- 368 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.31
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Transcriptional regulator ERG; DNA (5'-D(P*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)…
- UniProt
- P11308, Q13950, Q13951
- Ligands
- QWP, MG
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · resolution 4.31 · 5 distinct chains · 21% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator ERG | protein | 98 | 42% helix, 8% strand | P11308 |
| B | DNA (5'-D(P*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3') | dna | 16 | — | — |
| C | DNA (5'-D(P*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*TP*G)-3') | dna | 16 | — | — |
| D | Runt-related transcription factor 2 | protein | 117 | 0% helix, 37% strand | Q13950 |
| G | Core-binding factor subunit beta | protein | 121 | 26% helix, 25% strand | Q13951 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.70 | 0.81 | 37 | empty |
| 2 | 436 | 0.62 | 0.77 | 25 | empty |
| 3 | 175 | 0.61 | 0.84 | 23 | empty |
| 4 | 123 | 0.44 | 0.77 | 17 | empty |
| 5 | 111 | 0.43 | 0.77 | 16 | empty |
Interfaces
6 interfaces between chains.
- D–G · 1139 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 726 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- A–B · 517 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–C · 493 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–D · 408 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 6VGG · Crystal structure of the DNA binding domains of human transcription factor erg, human… · the same entry in another collection · chain G against G, TM-score 1.00
- Q13951 · AlphaFold monomer V2.0 prediction for core-binding factor subunit beta (Q13951) · a predicted model of the same protein · chain G against A, TM-score 0.98
- Q13950 · AlphaFold monomer V2.0 prediction for runt-related transcription factor 2 (Q13950) · a predicted model of the same protein · chain D against A, TM-score 0.97
- P11308 · AlphaFold monomer V2.0 prediction for transcriptional regulator erg (P11308) · a predicted model of the same protein · chain A against A, TM-score 0.87
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 P11308
- Every structure of UniProt Q13950
- Every structure of UniProt Q13951
- Elsewhere: RCSB PDB 6VGG · PDBe 6VGG · UniProt P11308 · UniProt Q13950 · UniProt Q13951
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