Research workbench
DNA binding domain of early B-cell factor 1 (EBF1) bound to DNA (crystal form II)
Analyse DNA binding domain of early B-cell factor 1 (EBF1) bound to DNA (crystal form… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MLN
- Type
- protein + DNA
- Length
- 627 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor COE1; DNA (5'- D(*CP*TP*TP*TP*AP*TP*TP*CP*CP*CP*AP*TP*GP*GP*GP*AP*AP*…
- UniProt
- Q07802
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription factor COE1 | protein | 206 | 14% helix, 40% strand | Q07802 |
| B | Transcription factor COE1 | protein | 213 | 14% helix, 38% strand | Q07802 |
| E | Transcription factor COE1 | protein | 164 | 5% helix, 52% strand | Q07802 |
| C, D | DNA (5'- D(*CP*TP*TP*TP*AP*TP*TP*CP*CP*CP*AP*TP*GP*GP*GP*AP*AP*TP*AP*AP*AP*G)- 3') | dna | 22 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.88 | 0.89 | 98 | empty |
| 2 | 53 | 0.50 | 0.87 | 12 | empty |
| 3 | 95 | 0.35 | 0.75 | 15 | empty |
| 4 | 92 | 0.35 | 0.75 | 16 | empty |
| 5 | 67 | 0.32 | 0.76 | 12 | empty |
Interfaces
9 interfaces between chains.
- C–D · 963 Ų buried · 95 hydrogen bonds · nucleic-nucleic
- B–C · 736 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–E · 726 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 721 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–C · 720 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 3MLN · DNA binding domain of Early B-cell Factor 1 (Ebf1) bound to DNA (crystal form II) · the same entry in another collection · chain D against D, TM-score 1.00
- Q07802 · AlphaFold monomer V2.0 prediction for transcription factor COE1 (Q07802) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q07802
- Elsewhere: RCSB PDB 3MLN · PDBe 3MLN · UniProt Q07802
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