MolNFT v1 · #106732 · protein + DNA
Structure of the human mineralocorticoid receptor in complex with DNA
4TNT: “Structure of the human mineralocorticoid receptor in complex with DNA”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.68). MolNFT v1 #106732 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4TNT
- Type
- protein + DNA
- Length
- 178 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mineralocorticoid receptor; DNA (5'- D(*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)…
- UniProt
- P08235
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mineralocorticoid receptor | protein | 72 | 31% helix, 8% strand | P08235 |
| C | DNA (5'- D(*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3') | dna | 17 | — | — |
| D | DNA (5'- D(*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3') | dna | 17 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 408 | 0.68 | 0.81 | 39 | empty |
| 2 | 69 | 0.34 | 0.76 | 14 | empty |
| 3 | 50 | 0.31 | 0.77 | 17 | empty |
| 4 | 51 | 0.31 | 0.77 | 11 | empty |
Interfaces
6 interfaces between chains.
- C–D · 778 Ų buried · 82 hydrogen bonds · nucleic-nucleic
- A–B · 602 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 401 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–C · 369 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–C · 294 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 4TNT · Structure of the human mineralocorticoid receptor in complex with DNA · the same entry in another collection · chain A against A, TM-score 1.00
- P08235 · AlphaFold monomer V2.0 prediction for mineralocorticoid receptor (P08235) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P08235
- Elsewhere: RCSB PDB 4TNT · PDBe 4TNT · UniProt P08235
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