Research workbench
Crystal structure of the yeast nicotinamidase PNC1P bound to the inhibitor nicotinaldehyde
Analyse Crystal structure of the yeast nicotinamidase PNC1P bound to the inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V8E
- Type
- protein
- Length
- 1,512 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinamidase
- EC
- 3.5.1.19
- UniProt
- P53184
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G | Nicotinamidase (EC 3.5.1.19) | protein | 216 | 32% helix, 27% strand | P53184 |
Ligands and binding sites
- ZN · Zinc ion · metal · 7 copies · chains A, B, C, D, E, F, G
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 659 | 0.71 | 0.78 | 47 | empty |
| 2 | 676 | 0.70 | 0.78 | 43 | empty |
| 3 | 683 | 0.70 | 0.77 | 47 | empty |
| 4 | 207 | 0.53 | 0.77 | 25 | empty |
| 5 | 228 | 0.52 | 0.76 | 23 | empty |
Interfaces
9 interfaces between chains.
- C–D · 629 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 599 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 598 Ų buried · 5 hydrogen bonds · protein-protein
- D–G · 585 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 574 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified (nonstandard).
Compared structures
- 3V8E · Crystal structure of the yeast nicotinamidase Pnc1p bound to the inhibitor nicotinaldehyde · the same entry in another collection · chain G against G, TM-score 1.00
- P53184 · AlphaFold monomer V2.0 prediction for nicotinamidase (P53184) · a predicted model of the same protein · 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 P53184
- Elsewhere: RCSB PDB 3V8E · PDBe 3V8E · UniProt P53184
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