Research workbench
Crystal structure of human peroxisomal coenzyme a diphosphatase NUDT7
Analyse Crystal structure of human peroxisomal coenzyme a diphosphatase NUDT7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T3P
- Type
- protein
- Length
- 660 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisomal coenzyme a diphosphatase NUDT7
- EC
- 3.6.1.-
- UniProt
- P0C024
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisomal coenzyme a diphosphatase NUDT7 (EC 3.6.1.-) | protein | 219 | 26% helix, 35% strand | P0C024 |
| B | Peroxisomal coenzyme a diphosphatase NUDT7 (EC 3.6.1.-) | protein | 220 | 29% helix, 35% strand | P0C024 |
| C | Peroxisomal coenzyme a diphosphatase NUDT7 (EC 3.6.1.-) | protein | 221 | 27% helix, 35% strand | P0C024 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.78 | 0.89 | 33 | empty |
| 2 | 942 | 0.78 | 0.80 | 94 | EDO |
| 3 | 474 | 0.76 | 0.84 | 62 | EDO |
| 4 | 364 | 0.74 | 0.84 | 50 | empty |
| 5 | 386 | 0.59 | 0.76 | 47 | empty |
Interfaces
3 interfaces between chains.
- B–C · 573 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 490 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 467 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5T3P · Crystal structure of Human Peroxisomal coenzyme A diphosphatase NUDT7 · the same entry in another collection · chain A against A, TM-score 1.00
- P0C024 · AlphaFold monomer V2.0 prediction for peroxisomal coenzyme a diphosphatase NUDT7 (P0C024) · a predicted model of the same protein · chain C 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 P0C024
- Elsewhere: RCSB PDB 5T3P · PDBe 5T3P · UniProt P0C024
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