MolNFT v1 · #136975 · protein + DNA
Glucocorticoid receptor DNA binding domain in complex with ap-1 response element from vcam-1 promoter
5VA0: “Glucocorticoid receptor DNA binding domain in complex with ap-1 response element from vcam-1 promoter”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.51). MolNFT v1 #136975 on GenesisL1: 3D structure, binding…
- PDB
- 5VA0
- Type
- protein + DNA
- Length
- 174 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucocorticoid receptor; DNA (5'-D(*CP*GP*GP*CP*TP*GP*AP*CP*TP*CP*AP*TP*CP*AP*AP*G)- 3')…
- UniProt
- P04150
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucocorticoid receptor | protein | 70 | 33% helix, 11% strand | P04150 |
| C | DNA (5'-D(*CP*GP*GP*CP*TP*GP*AP*CP*TP*CP*AP*TP*CP*AP*AP*G)- 3') | dna | 16 | — | — |
| D | DNA (5'-D(*CP*TP*TP*GP*AP*TP*GP*AP*GP*TP*CP*AP*GP*CP*CP*G)- 3') | dna | 16 | — | — |
| B | Glucocorticoid receptor | protein | 72 | 35% helix, 11% strand | P04150 |
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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.51 | 0.77 | 20 | empty |
| 2 | 154 | 0.39 | 0.73 | 19 | empty |
| 3 | 122 | 0.38 | 0.74 | 22 | empty |
| 4 | 70 | 0.33 | 0.76 | 13 | empty |
Interfaces
5 interfaces between chains.
- C–D · 730 Ų buried · 68 hydrogen bonds · nucleic-nucleic
- A–D · 340 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–C · 254 Ų buried · 7 hydrogen bonds · protein-nucleic
- D–B · 243 Ų buried · 5 hydrogen bonds · protein-nucleic
- C–B · 89 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 5VA0 · Glucocorticoid Receptor DNA Binding Domain in complex with AP-1 response element from… · 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 0.96
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 P04150
- Elsewhere: RCSB PDB 5VA0 · PDBe 5VA0 · UniProt P04150
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