MolNFT v1 · #88181 · protein + DNA
Crystal structure of the human retinoid X receptor DNA- binding domain bound to the human RAMP2 response element
4CN2 · 5'-D(*TP*GP*AP*GP*TP*TP*CP*AP*AP*GP*GP*GP*TP*DC…: “Crystal structure of the human retinoid X receptor DNA- binding domain bound to the human RAMP2 response…”. X-ray diffraction, 3 ligands (MG, ZN, CL), 5 pockets (best druggability…
- PDB
- 4CN2
- Type
- protein + DNA
- Length
- 197 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*GP*AP*GP*TP*TP*CP*AP*AP*GP*GP*GP*TP*DC *AP*AP*TP)-3'…
- UniProt
- P19793
- Ligands
- MG, ZN, CL
- Pockets
- 5 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-D(*TP*GP*AP*GP*TP*TP*CP*AP*AP*GP*GP*GP*TP*DC *AP*AP*TP)-3' | dna | 17 | — | — |
| B | 5'-D(*AP*TP*TP*GP*AP*CP*CP*CP*TP*TP*GP*AP*AP*DC *TP*CP*AP)-3' | dna | 17 | — | — |
| C | Retinoic acid receptor rxr-alpha | protein | 82 | 32% helix, 12% strand | P19793 |
| D | Retinoic acid receptor rxr-alpha | protein | 81 | 32% helix, 7% strand | P19793 |
Ligands and binding sites
- MG · Magnesium ion · metal · 7 copies · chains A, C, D, B
- ZN · Zinc ion · metal · 4 copies · chains C, D
- CL · Chloride ion · ion · 4 copies · chains C, D, A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains C
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 | 102 | 0.51 | 0.82 | 22 | empty |
| 2 | 206 | 0.49 | 0.76 | 21 | MG, CL |
| 3 | 105 | 0.47 | 0.80 | 18 | empty |
| 4 | 117 | 0.46 | 0.79 | 18 | MG |
| 5 | 71 | 0.35 | 0.77 | 16 | MG |
Interfaces
6 interfaces between chains.
- A–B · 758 Ų buried · 61 hydrogen bonds · nucleic-nucleic
- A–D · 530 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–D · 470 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–C · 460 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 410 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 4CN2 · Crystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to the Human… · the same entry in another collection · chain A against A, TM-score 1.00
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 P19793
- Elsewhere: RCSB PDB 4CN2 · PDBe 4CN2 · UniProt P19793
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