MolNFT v1 · #12250 · protein + DNA
Crystal structure of vdr DNA-binding domain bound to rat osteocalcin (oc) response element
1KB6 · 5'- D(*CP*AP*CP*GP*GP*GP*TP*GP*AP*AP*TP*GP*AP*GP*GP*AP*CP*A)…: “Crystal structure of vdr DNA-binding domain bound to rat osteocalcin (oc) response element”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.75).…
- PDB
- 1KB6
- Type
- protein + DNA
- Length
- 231 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(*CP*AP*CP*GP*GP*GP*TP*GP*AP*AP*TP*GP*AP*GP*GP*AP*CP*A)- 3'; 5'…
- UniProt
- P11473
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'- D(*CP*AP*CP*GP*GP*GP*TP*GP*AP*AP*TP*GP*AP*GP*GP*AP*CP*A)- 3' | dna | 18 | — | — |
| D | 5'- D(*TP*GP*TP*CP*CP*TP*CP*AP*TP*TP*CP*AP*CP*CP*CP*GP*TP*G)- 3' | dna | 18 | — | — |
| A | Vitamin D3 receptor | protein | 94 | 38% helix, 9% strand | P11473 |
| B | Vitamin D3 receptor | protein | 101 | 53% helix, 6% 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 | 709 | 0.75 | 0.81 | 43 | empty |
| 2 | 142 | 0.49 | 0.79 | 18 | empty |
| 3 | 107 | 0.44 | 0.78 | 13 | empty |
| 4 | 90 | 0.33 | 0.74 | 19 | empty |
| 5 | 76 | 0.31 | 0.74 | 18 | empty |
Interfaces
6 interfaces between chains.
- C–D · 821 Ų buried · 79 hydrogen bonds · nucleic-nucleic
- C–A · 522 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–A · 515 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–B · 418 Ų buried · 6 hydrogen bonds · protein-nucleic
- D–B · 398 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 1KB6 · Crystal Structure of VDR DNA-binding Domain Bound to Rat Osteocalcin (OC) Response Element · 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 1KB6 · PDBe 1KB6 · UniProt P11473
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