MolNFT v1 · #112046 · protein
Crystal structure of USP7 in complex with DNMT1(K1115Q)
4Z97 · Ubiquitin carboxyl-terminal hydrolase 7: “Crystal structure of USP7 in complex with DNMT1(K1115Q)”. X-ray diffraction, 8 pockets (best druggability 0.65). MolNFT v1 #112046 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4Z97
- Type
- protein
- Length
- 529 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 7; DNA (cytosine-5)-methyltransferase 1
- EC
- 3.4.19.12, 2.1.1.37
- UniProt
- Q93009
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 521 | 19% helix, 33% strand | Q93009 |
| C | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.65 | 0.84 | 27 | empty |
| 2 | 169 | 0.53 | 0.79 | 26 | empty |
| 3 | 93 | 0.44 | 0.79 | 21 | empty |
| 4 | 187 | 0.42 | 0.72 | 27 | empty |
| 5 | 103 | 0.39 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–C · 661 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4Z97 · Crystal structure of USP7 in complex with DNMT1(K1115Q) · the same entry in another collection · chain A against A, TM-score 1.00
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 Q93009
- Elsewhere: RCSB PDB 4Z97 · PDBe 4Z97 · UniProt Q93009
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