MolNFT v1 · #117377 · protein + DNA
Glucocorticoid receptor DNA binding domain - CCL2 nf-kb response element complex
5E6C: “Glucocorticoid receptor DNA binding domain - CCL2 nf-kb response element complex”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.68). MolNFT v1 #117377 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5E6C
- Type
- protein + DNA
- Length
- 182 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucocorticoid receptor; DNA (5'-D(*AP*GP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*AP*CP*T)- 3')…
- UniProt
- P04150
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucocorticoid receptor | protein | 78 | 29% helix, 10% strand | P04150 |
| B | Glucocorticoid receptor | protein | 72 | 31% helix, 11% strand | P04150 |
| C | DNA (5'-D(*AP*GP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*AP*CP*T)- 3') | dna | 16 | — | — |
| D | DNA (5'-D(*AP*GP*TP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*AP*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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.68 | 0.77 | 51 | empty |
| 2 | 89 | 0.35 | 0.75 | 20 | empty |
Interfaces
5 interfaces between chains.
- C–D · 702 Ų buried · 53 hydrogen bonds · nucleic-nucleic
- A–B · 602 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 406 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–D · 393 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–C · 228 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 5E6C · Glucocorticoid receptor DNA binding domain - CCL2 NF-kB response 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 B 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 5E6C · PDBe 5E6C · UniProt P04150
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