Research workbench
Data-driven model of MED1:DNA complex
Analyse Data-driven model of MED1:DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2KAE
- Type
- protein + DNA
- Length
- 96 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gata-type transcription factor; 5'-D(*DCP*DGP*DGP*DAP*DAP*DAP*DAP*DGP*DTP*DAP*DTP*DAP*DCP*…
- UniProt
- Q9GSP3
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.58
Structure
solution nmr · 2 distinct chains · 36% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gata-type transcription factor | protein | 56 | 36% helix, 0% strand | Q9GSP3 |
| C, B | 5'-D(*DCP*DGP*DGP*DAP*DAP*DAP*DAP*DGP*DTP*DAP*DTP*DAP*DCP*D TP*DTP*DTP*DTP*DCP*DCP*DG)-3' | dna | 20 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
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 | 63 | 0.58 | 0.90 | 16 | empty |
| 2 | 130 | 0.37 | 0.74 | 13 | empty |
| 3 | 51 | 0.25 | 0.74 | 11 | empty |
Interfaces
3 interfaces between chains.
- C–B · 893 Ų buried · 89 hydrogen bonds · nucleic-nucleic
- A–B · 868 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–C · 799 Ų buried · 20 hydrogen bonds · protein-nucleic
Compared structures
- 2KAE · data-driven model of MED1:DNA complex · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9GSP3
- Elsewhere: RCSB PDB 2KAE · PDBe 2KAE · UniProt Q9GSP3
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