MolNFT v1 · #12248 · protein + DNA
Crystal structure of vdr DNA-binding domain bound to a canonical direct repeat with three base pair spacer (DR3) response element
1KB4 · 5'- D(*CP*AP*CP*AP*GP*GP*TP*CP*AP*CP*GP*AP*AP*GP*GP*TP*CP*A)…: “Crystal structure of vdr DNA-binding domain bound to a canonical direct repeat with three base pair spacer…”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best…
- PDB
- 1KB4
- Type
- protein + DNA
- Length
- 228 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(*CP*AP*CP*AP*GP*GP*TP*CP*AP*CP*GP*AP*AP*GP*GP*TP*CP*A)- 3'; 5'…
- UniProt
- P11473
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'- D(*CP*AP*CP*AP*GP*GP*TP*CP*AP*CP*GP*AP*AP*GP*GP*TP*CP*A)- 3' | dna | 18 | — | — |
| D | 5'- D(*TP*GP*AP*CP*CP*TP*TP*CP*GP*TP*GP*AP*CP*CP*TP*GP*TP*G)- 3' | dna | 18 | — | — |
| A | Vitamin D3 receptor | protein | 93 | 38% helix, 6% strand | P11473 |
| B | Vitamin D3 receptor | protein | 99 | 46% helix, 8% strand | P11473 |
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 | 722 | 0.76 | 0.81 | 44 | empty |
| 2 | 190 | 0.44 | 0.74 | 17 | empty |
| 3 | 67 | 0.37 | 0.79 | 11 | empty |
| 4 | 66 | 0.29 | 0.74 | 15 | empty |
| 5 | 64 | 0.27 | 0.73 | 12 | empty |
Interfaces
6 interfaces between chains.
- C–D · 823 Ų buried · 79 hydrogen bonds · nucleic-nucleic
- D–A · 505 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–A · 463 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–B · 386 Ų buried · 5 hydrogen bonds · protein-nucleic
- D–B · 364 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 1KB4 · Crystal Structure of VDR DNA-binding Domain Bound to a Canonical Direct Repeat with Three… · the same entry in another collection · chain C against C, TM-score 1.00
- P11473 · AlphaFold monomer V2.0 prediction for vitamin D3 receptor (P11473) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P11473
- Elsewhere: RCSB PDB 1KB4 · PDBe 1KB4 · UniProt P11473
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