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Pandda analysis group deposition of models with modelled events (E.G. bound ligands) -- crystal structure of NUDT7 in complex with FMOPL000609A
Analyse Pandda analysis group deposition of models with modelled events (E.G. bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5QGT
- Type
- protein
- Length
- 186 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisomal coenzyme a diphosphatase NUDT7
- EC
- 3.6.1.-
- UniProt
- P0C024
- Ligands
- H04
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisomal coenzyme a diphosphatase NUDT7 (EC 3.6.1.-) | protein | 186 | 25% helix, 36% strand | P0C024 |
Ligands and binding sites
- H04 · 1-(2-ethoxyphenyl)piperazine · ligand · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.53 | 0.79 | 25 | H04 |
| 2 | 89 | 0.36 | 0.75 | 18 | empty |
Modifications
Observed in the structure: 2 modified (hydroxylation, oxidation).
Compared structures
- 5QGT · PanDDA analysis group deposition of models with modelled events (e.g. bound ligands)… · 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 A against A, TM-score 0.95
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 5QGT · PDBe 5QGT · UniProt P0C024
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