Research workbench
Glucocorticoid receptor DNA binding domain in complex with unmodified precursor for a modern recognition element (pre-gbs)
Analyse Glucocorticoid receptor DNA binding domain in complex with unmodified precursor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X6D
- Type
- protein + DNA
- Length
- 183 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucocorticoid receptor; DNA (5'- D(*CP*CP*AP*GP*AP*AP*CP*GP*GP*AP*GP*CP*GP*TP*TP*CP*TP*G)…
- UniProt
- P04150
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucocorticoid receptor | protein | 74 | 31% helix, 11% strand | P04150 |
| B | Glucocorticoid receptor | protein | 73 | 34% helix, 11% strand | P04150 |
| C | DNA (5'- D(*CP*CP*AP*GP*AP*AP*CP*GP*GP*AP*GP*CP*GP*TP*TP*CP*TP*G)-3') | dna | 18 | — | — |
| D | DNA (5'- D(*TP*CP*AP*GP*AP*AP*CP*GP*CP*TP*CP*CP*GP*TP*TP*CP*TP*G)-3') | dna | 18 | — | — |
Ligands and binding sites
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 | 624 | 0.71 | 0.79 | 51 | CAC |
| 2 | 73 | 0.32 | 0.75 | 18 | empty |
| 3 | 72 | 0.30 | 0.74 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–D · 785 Ų buried · 85 hydrogen bonds · nucleic-nucleic
- A–B · 605 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 376 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–D · 373 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–C · 324 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 6X6D · Glucocorticoid Receptor DNA binding domain in complex with unmodified precursor for a… · 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 6X6D · PDBe 6X6D · UniProt P04150
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