Research workbench
Crystal structure of the homodimeric mafb in complex with the T-mare binding site
Analyse Crystal structure of the homodimeric mafb in complex with the T-mare binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WTY
- Type
- protein + DNA
- Length
- 230 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor mafb; DNA (5'-D(*TP*AP*AP*TP*TP*GP*CP*TP*GP*AP*CP*TP*CP*AP…
- UniProt
- P54841
- Ligands
- MG
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 86% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription factor mafb | protein | 94 | 85% helix, 0% strand | P54841 |
| B | Transcription factor mafb | protein | 97 | 88% helix, 0% strand | P54841 |
| C | DNA (5'-D(*TP*AP*AP*TP*TP*GP*CP*TP*GP*AP*CP*TP*CP*AP *GP*CP*AP*AP*AP*T)-3') | dna | 20 | — | — |
| D | DNA (5'-D(*TP*AP*TP*TP*TP*GP*CP*TP*GP*AP*GP*TP*CP*AP *GP*CP*AP*AP*TP*T)-3') | dna | 19 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.70 | 0.84 | 31 | empty |
| 2 | 115 | 0.44 | 0.77 | 18 | empty |
| 3 | 71 | 0.40 | 0.79 | 13 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1350 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 838 Ų buried · 86 hydrogen bonds · nucleic-nucleic
- A–D · 441 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 401 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–D · 361 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 2WTY · Crystal structure of the homodimeric MafB in complex with the T-MARE binding site · the same entry in another collection · chain A against A, TM-score 1.00
- P54841 · AlphaFold monomer V2.0 prediction for transcription factor mafb (P54841) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 P54841
- Elsewhere: RCSB PDB 2WTY · PDBe 2WTY · UniProt P54841
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