MolNFT v1 · #81969 · protein
Crystal structure of the yeast nicotinamidase PNC1P bound to the inhibitor nicotinaldehyde
3V8E: “Crystal structure of the yeast nicotinamidase PNC1P bound to the inhibitor nicotinaldehyde”. X-ray diffraction, 2 ligands (ZN, MG), 20 pockets (best druggability 0.71). MolNFT v1 #81969 on GenesisL1: 3D structure, binding sites and…
- 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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