MolNFT v1 · #95799 · protein + DNA
Structure of a novel telomere repeat binding protein bound to DNA
4J19 · Homeobox-containing protein 1: “Structure of a novel telomere repeat binding protein bound to DNA”. X-ray diffraction, 1 ligand (CL), 4 pockets (best druggability 0.62). MolNFT v1 #95799 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4J19
- Type
- protein + DNA
- Length
- 191 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homeobox-containing protein 1; DNA (5'- D(*CP*TP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP…
- UniProt
- Q6NT76
- Ligands
- CL
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homeobox-containing protein 1 | protein | 77 | 61% helix, 0% strand | Q6NT76 |
| B | Homeobox-containing protein 1 | protein | 76 | 61% helix, 0% strand | Q6NT76 |
| C | DNA (5'- D(*CP*TP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3') | dna | 19 | — | — |
| D | DNA (5'- D(*TP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*A)-3') | dna | 19 | — | — |
Ligands and binding sites
- CL · Chloride ion · ion · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.62 | 0.77 | 45 | CL |
| 2 | 79 | 0.39 | 0.78 | 16 | empty |
| 3 | 105 | 0.38 | 0.75 | 18 | empty |
| 4 | 63 | 0.32 | 0.76 | 12 | empty |
Interfaces
6 interfaces between chains.
- C–D · 806 Ų buried · 68 hydrogen bonds · nucleic-nucleic
- B–C · 585 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–D · 530 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–C · 386 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–D · 364 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 4J19 · Structure of a novel telomere repeat binding protein bound to DNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q6NT76 · AlphaFold monomer V2.0 prediction for homeobox-containing protein 1 (Q6NT76) · a predicted model of the same protein · chain A 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 Q6NT76
- Elsewhere: RCSB PDB 4J19 · PDBe 4J19 · UniProt Q6NT76
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