MolNFT v1 · #169266 · protein + DNA
Glucocorticoid receptor DNA binding domain in complex with methylated precursor for a modern recognition element (methylated pre-gbs)
6X6E: “Glucocorticoid receptor DNA binding domain in complex with methylated precursor for a modern recognition…”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.73). MolNFT v1 #169266 on GenesisL1: 3D structure, binding…
- PDB
- 6X6E
- Type
- protein + DNA
- Length
- 180 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*(5CM)…
- UniProt
- P04150
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucocorticoid receptor | protein | 73 | 32% helix, 11% strand | P04150 |
| B | Glucocorticoid receptor | protein | 71 | 34% helix, 11% strand | P04150 |
| C | DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*GP*GP*AP*GP*(5CM) P*GP*TP*TP*CP*TP*G)-3') | dna | 18 | — | — |
| D | DNA (5'-D(*TP*CP*AP*GP*AP*AP*CP*GP*CP*TP*CP*(5CM) P*GP*TP*TP*CP*TP*G)-3') | dna | 18 | — | — |
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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 747 | 0.73 | 0.79 | 63 | empty |
| 2 | 73 | 0.32 | 0.75 | 18 | empty |
| 3 | 70 | 0.31 | 0.75 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–D · 789 Ų buried · 68 hydrogen bonds · nucleic-nucleic
- A–B · 564 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 391 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–D · 335 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–C · 305 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6X6E · Glucocorticoid Receptor DNA binding domain in complex with methylated 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 0.96
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 6X6E · PDBe 6X6E · UniProt P04150
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