Research workbench
Glucocorticoid receptor DNA binding domain - ICAM1 nf-kb response element complex
Analyse Glucocorticoid receptor DNA binding domain - ICAM1 nf-kb response element… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E6D
- Type
- protein + DNA
- Length
- 177 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*CP*TP*CP*CP*GP*GP*AP*AP*TP*TP*TP*CP*CP*AP*A)- 3'); DNA…
- UniProt
- P04150
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'-D(*GP*CP*TP*CP*CP*GP*GP*AP*AP*TP*TP*TP*CP*CP*AP*A)- 3') | dna | 16 | — | — |
| D | DNA (5'-D(*TP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*GP*GP*AP*GP*C)- 3') | dna | 16 | — | — |
| A | Glucocorticoid receptor | protein | 73 | 32% helix, 11% strand | P04150 |
| B | Glucocorticoid receptor | protein | 72 | 18% helix, 11% strand | P04150 |
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 | 610 | 0.69 | 0.78 | 41 | empty |
| 2 | 124 | 0.40 | 0.75 | 19 | empty |
| 3 | 98 | 0.36 | 0.75 | 18 | empty |
Interfaces
5 interfaces between chains.
- C–D · 683 Ų buried · 63 hydrogen bonds · nucleic-nucleic
- A–B · 619 Ų buried · 10 hydrogen bonds · protein-protein
- D–A · 329 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–A · 282 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–B · 176 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 5E6D · Glucocorticoid receptor DNA binding domain - ICAM1 NF-kB response element complex · the same entry in another collection · chain C against C, 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 5E6D · PDBe 5E6D · UniProt P04150
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