Research workbench
DNA binding domain of early B-cell factor 1 (EBF1) bound to DNA (crystal form I)
Analyse DNA binding domain of early B-cell factor 1 (EBF1) bound to DNA (crystal form I) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MLO
- Type
- protein + DNA
- Length
- 469 residues
- Chains
- 4
- 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
- 4 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription factor COE1 | protein | 212 | 11% helix, 39% strand | Q07802 |
| B | Transcription factor COE1 | protein | 213 | 7% helix, 37% 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1131 | 0.85 | 0.86 | 86 | empty |
| 2 | 286 | 0.55 | 0.77 | 38 | empty |
| 3 | 94 | 0.39 | 0.77 | 20 | empty |
| 4 | 64 | 0.33 | 0.77 | 11 | empty |
Interfaces
6 interfaces between chains.
- C–D · 955 Ų buried · 90 hydrogen bonds · nucleic-nucleic
- B–D · 748 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–C · 724 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–D · 718 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–C · 712 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 3MLO · DNA binding domain of Early B-cell Factor 1 (Ebf1) bound to DNA (Crystal form I) · the same entry in another collection · chain A against A, 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 0.97
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 3MLO · PDBe 3MLO · UniProt Q07802
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