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Crystal structure of nicotinate-nucleotide pyrophosphorylase from pyrococcus furiosus
Analyse Crystal structure of nicotinate-nucleotide pyrophosphorylase from pyrococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2I14
- Type
- protein
- Length
- 2,334 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinate-nucleotide pyrophosphorylase
- UniProt
- Q8TZS9
- Ligands
- PCP, ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Nicotinate-nucleotide pyrophosphorylase | protein | 389 | 40% helix, 20% strand | Q8TZS9 |
Ligands and binding sites
- PCP · 1-alpha-pyrophosphoryl-2-alpha,3-alpha-dihydroxy-4-beta-cyclopentane-methanol-5-phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 775 | 0.83 | 0.86 | 84 | ZN, PCP |
| 2 | 675 | 0.82 | 0.86 | 75 | PCP |
| 3 | 643 | 0.82 | 0.86 | 68 | PCP |
| 4 | 637 | 0.81 | 0.86 | 68 | PCP |
| 5 | 553 | 0.81 | 0.87 | 57 | PCP |
Interfaces
15 interfaces between chains.
- C–D · 4889 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 4872 Ų buried · 47 hydrogen bonds · protein-protein
- E–F · 4844 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 611 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 605 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2I14 · Crystal structure of nicotinate-nucleotide pyrophosphorylase from Pyrococcus furiosus · the same entry in another collection · 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 Q8TZS9
- Elsewhere: RCSB PDB 2I14 · PDBe 2I14 · UniProt Q8TZS9
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