Research workbench
Glucocorticoid receptor DNA binding domain - IL11 ap-1 recognition element complex
Analyse Glucocorticoid receptor DNA binding domain - IL11 ap-1 recognition element… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VA7
- Type
- protein + DNA
- Length
- 172 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucocorticoid receptor; DNA (5'-D(*AP*GP*GP*GP*TP*GP*AP*GP*TP*CP*AP*GP*GP*AP*TP*G)- 3')…
- UniProt
- P04150
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.46
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glucocorticoid receptor | protein | 70 | 33% helix, 11% strand | P04150 |
| C | DNA (5'-D(*AP*GP*GP*GP*TP*GP*AP*GP*TP*CP*AP*GP*GP*AP*TP*G)- 3') | dna | 16 | — | — |
| D | DNA (5'-D(*CP*AP*TP*CP*CP*TP*GP*AP*CP*TP*CP*AP*CP*CP*CP*T)- 3') | dna | 16 | — | — |
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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.46 | 0.74 | 29 | empty |
| 2 | 203 | 0.46 | 0.74 | 21 | empty |
| 3 | 109 | 0.40 | 0.76 | 19 | empty |
Interfaces
5 interfaces between chains.
- C–D · 724 Ų buried · 70 hydrogen bonds · nucleic-nucleic
- A–D · 311 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–C · 282 Ų buried · 6 hydrogen bonds · protein-nucleic
- D–B · 223 Ų buried · 5 hydrogen bonds · protein-nucleic
- C–B · 43 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 5VA7 · Glucocorticoid Receptor DNA Binding Domain - IL11 AP-1 recognition element Complex · the same entry in another collection · chain A against A, TM-score 1.00
- P04150 · AlphaFold monomer V2.0 prediction for glucocorticoid receptor (P04150) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P04150
- Elsewhere: RCSB PDB 5VA7 · PDBe 5VA7 · UniProt P04150
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