Research workbench
Hlrh-1 DNA binding domain - 12BP OCT4 promoter complex
Analyse Hlrh-1 DNA binding domain - 12BP OCT4 promoter complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L0M
- Type
- protein + DNA
- Length
- 120 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor subfamily 5 group a member 2; DNA…
- UniProt
- O00482
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor subfamily 5 group a member 2 | protein | 96 | 31% helix, 11% strand | O00482 |
| C | DNA (5'-D(*CP*TP*AP*GP*CP*CP*TP*TP*GP*AP*CP*C)-3') | dna | 12 | — | — |
| B | DNA (5'-D(*GP*GP*TP*CP*AP*AP*GP*GP*CP*TP*AP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.38 | 0.76 | 14 | empty |
| 2 | 60 | 0.30 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 694 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–B · 649 Ų buried · 19 hydrogen bonds · protein-nucleic
- C–B · 542 Ų buried · 44 hydrogen bonds · nucleic-nucleic
Compared structures
- 5L0M · hLRH-1 DNA Binding Domain - 12bp Oct4 promoter complex · the same entry in another collection · chain A against A, TM-score 1.00
- O00482 · AlphaFold monomer V2.0 prediction for nuclear receptor subfamily 5 group a member 2… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 O00482
- Elsewhere: RCSB PDB 5L0M · PDBe 5L0M · UniProt O00482
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