Research workbench
Structural basis of NR4A1 bound to the human pituitary proopiomelanocortin gene promoter
Analyse Structural basis of NR4A1 bound to the human pituitary proopiomelanocortin gene… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LC1
- Type
- protein + DNA
- Length
- 446 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA; Nuclear receptor subfamily 4 group a member 1; DNA (25-mer)
- UniProt
- P22736
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.48
Structure
x-ray diffraction · 5 distinct chains · 31% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I, F | DNA | dna | 26 | — | — |
| J, D | Nuclear receptor subfamily 4 group a member 1 | protein | 86 | 26% helix, 7% strand | P22736 |
| L | DNA (25-mer) | dna | 25 | — | — |
| A, G | Nuclear receptor subfamily 4 group a member 1 | protein | 86 | 37% helix, 7% strand | P22736 |
| C | DNA (25-mer) | dna | 25 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains J, A, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.48 | 0.79 | 23 | empty |
| 2 | 85 | 0.44 | 0.80 | 22 | empty |
| 3 | 93 | 0.41 | 0.78 | 21 | empty |
| 4 | 113 | 0.38 | 0.75 | 15 | empty |
| 5 | 79 | 0.31 | 0.74 | 17 | empty |
Interfaces
16 interfaces between chains.
- I–L · 1094 Ų buried · 103 hydrogen bonds · nucleic-nucleic
- C–F · 1068 Ų buried · 105 hydrogen bonds · nucleic-nucleic
- D–F · 694 Ų buried · 20 hydrogen bonds · protein-nucleic
- I–G · 680 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 668 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 6LC1 · Structural basis of NR4A1 bound to the human pituitary proopiomelanocortin gene promoter · the same entry in another collection · chain G against G, TM-score 1.00
- P22736 · AlphaFold monomer V2.0 prediction for nuclear receptor subfamily 4 group a member 1… · a predicted model of the same protein · chain J against A, TM-score 0.87
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 P22736
- Elsewhere: RCSB PDB 6LC1 · PDBe 6LC1 · UniProt P22736
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