MolNFT v1 · #155579 · protein + DNA
Structural basis of NR4A1 bound to the human pituitary proopiomelanocortin gene promoter
6LC1 · DNA: “Structural basis of NR4A1 bound to the human pituitary proopiomelanocortin gene promoter”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.48). MolNFT v1 #155579 on GenesisL1: 3D structure, binding sites and…
- 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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