Research workbench
S425G glucocorticoid receptor DNA binding domain - (+)gre complex
Analyse S425G glucocorticoid receptor DNA binding domain - (+)gre complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CC1
- Type
- protein + DNA
- Length
- 368 residues
- Chains
- 8
- 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*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)…
- UniProt
- P04150
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, W | Glucocorticoid receptor | protein | 75 | 35% helix, 11% strand | P04150 |
| B, X | Glucocorticoid receptor | protein | 73 | 34% helix, 11% strand | P04150 |
| C, Z | DNA (5'- D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3') | dna | 18 | — | — |
| D, Y | DNA (5'- D(*TP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3') | dna | 18 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, W, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 563 | 0.70 | 0.79 | 42 | empty |
| 2 | 604 | 0.69 | 0.78 | 48 | empty |
| 3 | 298 | 0.61 | 0.79 | 50 | empty |
| 4 | 64 | 0.36 | 0.78 | 13 | empty |
| 5 | 60 | 0.35 | 0.78 | 12 | empty |
Interfaces
15 interfaces between chains.
- C–D · 784 Ų buried · 71 hydrogen bonds · nucleic-nucleic
- Y–Z · 783 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- A–B · 583 Ų buried · 10 hydrogen bonds · protein-protein
- W–X · 582 Ų buried · 10 hydrogen bonds · protein-protein
- B–W · 397 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- P04150 · AlphaFold monomer V2.0 prediction for glucocorticoid receptor (P04150) · a predicted model of the same protein · chain B 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 5CC1 · PDBe 5CC1 · UniProt P04150
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