MolNFT v1 · #122901 · protein + DNA
Crystal structure of human THYN1 protein in complex with 5- methylcytosine containing DNA
5J3E · Thymocyte nuclear protein 1: “Crystal structure of human THYN1 protein in complex with 5- methylcytosine containing DNA”. X-ray diffraction, 1 ligand (UNX), 3 pockets (best druggability 0.76). MolNFT v1 #122901 on GenesisL1: 3D…
- PDB
- 5J3E
- Type
- protein + DNA
- Length
- 391 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymocyte nuclear protein 1; 5-methylcytosine containing DNA
- UniProt
- Q9P016
- Ligands
- UNX
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymocyte nuclear protein 1 | protein | 172 | 29% helix, 31% strand | Q9P016 |
| B | Thymocyte nuclear protein 1 | protein | 171 | 31% helix, 31% strand | Q9P016 |
| C, D, E, F | 5-methylcytosine containing DNA | dna | 12 | — | — |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 8 copies · chains A, B, E, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.76 | 0.84 | 47 | UNX |
| 2 | 500 | 0.71 | 0.81 | 42 | UNX |
| 3 | 58 | 0.36 | 0.79 | 14 | empty |
Interfaces
7 interfaces between chains.
- E–F · 540 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- C–D · 536 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- A–E · 391 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–D · 364 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–B · 330 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 5J3E · Crystal Structure of Human THYN1 protein in complex with 5-methylcytosine containing DNA · the same entry in another collection · chain F against F, TM-score 1.00
- Q9P016 · AlphaFold monomer V2.0 prediction for thymocyte nuclear protein 1 (Q9P016) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9P016
- Elsewhere: RCSB PDB 5J3E · PDBe 5J3E · UniProt Q9P016
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