MolNFT v1 · #45817 · protein + DNA
Retinoid X receptor-thyroid hormone receptor DNA-binding domain heterodimer bound to thyroid response element DNA
2NLL · DNA (5'-D(*CP*AP*GP*GP*TP*CP*AP*TP*TP*(5IU)…: “Retinoid X receptor-thyroid hormone receptor DNA-binding domain heterodimer bound to thyroid response element…”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.68).…
- PDB
- 2NLL
- Type
- protein + DNA
- Length
- 205 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*AP*GP*GP*TP*CP*AP*TP*TP*(5IU) P*CP*AP*GP*GP*TP*CP*AP*G)-3'); DNA (5'…
- UniProt
- P19793, P10828
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'-D(*CP*AP*GP*GP*TP*CP*AP*TP*TP*(5IU) P*CP*AP*GP*GP*TP*CP*AP*G)-3') | dna | 18 | — | — |
| D | DNA (5'- D(*CP*TP*GP*AP*CP*CP*TP*GP*AP*AP*AP*TP*GP*AP*CP*CP*T P*G)- 3') | dna | 18 | — | — |
| A | Protein (retinoic acid receptor) | protein | 66 | 33% helix, 6% strand | P19793 |
| B | Protein (thyroid hormone receptor) | protein | 103 | 49% helix, 6% strand | P10828 |
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
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 | 722 | 0.68 | 0.77 | 53 | empty |
| 2 | 109 | 0.46 | 0.80 | 15 | empty |
| 3 | 167 | 0.46 | 0.76 | 28 | empty |
Interfaces
6 interfaces between chains.
- C–D · 810 Ų buried · 77 hydrogen bonds · nucleic-nucleic
- D–B · 599 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–B · 514 Ų buried · 12 hydrogen bonds · protein-nucleic
- D–A · 381 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–B · 285 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2NLL · Retinoid X receptor-thyroid hormone receptor DNA-binding domain heterodimer bound to… · the same entry in another collection · chain C against C, TM-score 1.00
- P10828 · AlphaFold monomer V2.0 prediction for thyroid hormone receptor beta (P10828) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P19793
- Every structure of UniProt P10828
- Elsewhere: RCSB PDB 2NLL · PDBe 2NLL · UniProt P19793 · UniProt P10828
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