MolNFT v1 · #111352 · protein
Crystal structure of human DNMT1 and USP7/HAUSP complex
4YOC · DNA (cytosine-5)-methyltransferase 1: “Crystal structure of human DNMT1 and USP7/HAUSP complex”. X-ray diffraction, 1 ligand (ZN), 17 pockets (best druggability 0.74). MolNFT v1 #111352 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4YOC
- Type
- protein
- Length
- 1,411 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 1; Ubiquitin carboxyl-terminal hydrolase 7
- EC
- 2.1.1.37, 3.4.19.12
- UniProt
- P26358, Q93009
- Ligands
- ZN
- Pockets
- 17 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 882 | 23% helix, 26% strand | P26358 |
| C | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 529 | 22% helix, 33% strand | Q93009 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.74 | 0.77 | 82 | empty |
| 2 | 796 | 0.73 | 0.79 | 67 | empty |
| 3 | 1196 | 0.73 | 0.76 | 112 | empty |
| 4 | 607 | 0.72 | 0.79 | 55 | empty |
| 5 | 215 | 0.59 | 0.80 | 28 | empty |
Interfaces
1 interface between chains.
- A–C · 1848 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 4YOC · Crystal Structure of human DNMT1 and USP7/HAUSP complex · the same entry in another collection · chain A against A, TM-score 1.00
- P26358 · AlphaFold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 1 (P26358) · 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 P26358
- Every structure of UniProt Q93009
- Elsewhere: RCSB PDB 4YOC · PDBe 4YOC · UniProt P26358 · UniProt Q93009
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