Research workbench
Crystal structure of unliganded sra domain of mouse NP95
Analyse Crystal structure of unliganded sra domain of mouse NP95 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZKG
- Type
- protein
- Length
- 747 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase UHRF1
- EC
- 6.3.2.-
- UniProt
- Q8VDF2
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | E3 ubiquitin-protein ligase UHRF1 (EC 6.3.2.-) | protein | 190 | 17% helix, 28% strand | Q8VDF2 |
| C | E3 ubiquitin-protein ligase UHRF1 (EC 6.3.2.-) | protein | 183 | 18% helix, 28% strand | Q8VDF2 |
| D | E3 ubiquitin-protein ligase UHRF1 (EC 6.3.2.-) | protein | 184 | 18% helix, 28% strand | Q8VDF2 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.74 | 0.81 | 44 | empty |
| 2 | 400 | 0.60 | 0.76 | 43 | empty |
| 3 | 471 | 0.57 | 0.73 | 61 | EDO |
| 4 | 289 | 0.56 | 0.76 | 32 | EDO |
| 5 | 113 | 0.53 | 0.82 | 30 | empty |
Interfaces
5 interfaces between chains.
- A–C · 497 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 268 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 154 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 129 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 33 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2ZKG · Crystal structure of unliganded SRA domain of mouse Np95 · the same entry in another collection · chain A against A, TM-score 1.00
- Q8VDF2 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase UHRF1 (Q8VDF2) · a predicted model of the same protein · chain C 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 Q8VDF2
- Elsewhere: RCSB PDB 2ZKG · PDBe 2ZKG · UniProt Q8VDF2
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