MolNFT v1 · #117911 · protein + DNA
Transcription factor grdbd and smgre complex
5EMC · DNA (5'-D(*CP*CP*AP*GP*AP*AP*(5CM)…: “Transcription factor grdbd and smgre complex”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.69). MolNFT v1 #117911 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5EMC
- Type
- protein + DNA
- Length
- 178 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*CP*AP*GP*AP*AP*(5CM) P*AP*TP*CP*AP*TP*GP*TP*TP*(5CM)P*TP*G)-3')…
- UniProt
- P04150
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'-D(*CP*CP*AP*GP*AP*AP*(5CM) P*AP*TP*CP*AP*TP*GP*TP*TP*(5CM)P*TP*G)-3') | dna | 18 | — | — |
| A | Glucocorticoid receptor | protein | 70 | 36% helix, 11% strand | P04150 |
| B | Glucocorticoid receptor | protein | 72 | 32% helix, 11% strand | P04150 |
| D | DNA (5'-D(*CP*CP*AP*GP*AP*AP*(5CM) P*AP*TP*GP*AP*TP*GP*TP*TP*(5CM)P*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
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.69 | 0.79 | 54 | empty |
| 2 | 105 | 0.39 | 0.76 | 19 | empty |
| 3 | 63 | 0.35 | 0.78 | 9 | empty |
| 4 | 51 | 0.34 | 0.79 | 12 | empty |
| 5 | 67 | 0.34 | 0.77 | 18 | empty |
Interfaces
6 interfaces between chains.
- C–D · 813 Ų buried · 81 hydrogen bonds · nucleic-nucleic
- A–B · 606 Ų buried · 11 hydrogen bonds · protein-protein
- C–B · 343 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–D · 332 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–D · 316 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
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 5EMC · PDBe 5EMC · UniProt P04150
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