MolNFT v1 · #12246 · protein + DNA
Crystal structure of vdr DNA-binding domain bound to mouse osteopontin (spp) response element
1KB2 · 5'- D(*CP*AP*CP*GP*GP*TP*TP*CP*AP*CP*GP*AP*GP*GP*TP*TP*CP*A)…: “Crystal structure of vdr DNA-binding domain bound to mouse osteopontin (spp) response element”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.74).…
- PDB
- 1KB2
- Type
- protein + DNA
- Length
- 210 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(*CP*AP*CP*GP*GP*TP*TP*CP*AP*CP*GP*AP*GP*GP*TP*TP*CP*A)- 3'; 5'…
- UniProt
- P11473
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'- D(*CP*AP*CP*GP*GP*TP*TP*CP*AP*CP*GP*AP*GP*GP*TP*TP*CP*A)- 3' | dna | 18 | — | — |
| D | 5'- D(*TP*GP*AP*AP*CP*CP*TP*CP*GP*TP*GP*AP*AP*CP*CP*GP*TP*G)- 3' | dna | 18 | — | — |
| A | Vitamin D3 receptor | protein | 89 | 40% helix, 7% strand | P11473 |
| B | Vitamin D3 receptor | protein | 85 | 42% helix, 7% 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 | 599 | 0.74 | 0.81 | 46 | empty |
| 2 | 97 | 0.41 | 0.78 | 14 | empty |
| 3 | 88 | 0.31 | 0.73 | 11 | empty |
| 4 | 82 | 0.30 | 0.73 | 19 | empty |
| 5 | 58 | 0.28 | 0.75 | 16 | empty |
Interfaces
6 interfaces between chains.
- C–D · 826 Ų buried · 70 hydrogen bonds · nucleic-nucleic
- D–A · 489 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–A · 477 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–B · 377 Ų buried · 5 hydrogen bonds · protein-nucleic
- D–B · 362 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 1KB2 · Crystal Structure of VDR DNA-binding Domain Bound to Mouse Osteopontin (SPP) Response… · 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 0.97
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 1KB2 · PDBe 1KB2 · UniProt P11473
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