Research workbench
Crystal structure of the ampcpr-bound ATNUDT7
Analyse Crystal structure of the ampcpr-bound ATNUDT7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZBP
- Type
- protein
- Length
- 790 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nudix hydrolase 7
- EC
- 3.6.1.-, 3.6.1.13, 3.6.1.22
- UniProt
- Q9SU14
- Ligands
- ADV, SO4
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nudix hydrolase 7 (EC 3.6.1.-, 3.6.1.13, 3.6.1.22) | protein | 258 | 27% helix, 33% strand | Q9SU14 |
| B | Nudix hydrolase 7 (EC 3.6.1.-, 3.6.1.13, 3.6.1.22) | protein | 270 | 30% helix, 34% strand | Q9SU14 |
| C | Nudix hydrolase 7 (EC 3.6.1.-, 3.6.1.13, 3.6.1.22) | protein | 262 | 27% helix, 32% strand | Q9SU14 |
Ligands and binding sites
- ADV · Alpha-beta methylene adp-ribose · ligand · chains C
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.73 | 0.76 | 99 | empty |
| 2 | 307 | 0.61 | 0.79 | 41 | empty |
| 3 | 391 | 0.55 | 0.74 | 48 | empty |
| 4 | 287 | 0.51 | 0.74 | 30 | empty |
| 5 | 109 | 0.46 | 0.79 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–B · 3560 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 217 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 Q9SU14
- Elsewhere: RCSB PDB 4ZBP · PDBe 4ZBP · UniProt Q9SU14
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