Research workbench
Crystal structure of human quinolinate phosphoribosyltransferase in complex with the product nicotinate mononucleotide
Analyse Crystal structure of human quinolinate phosphoribosyltransferase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AYZ
- Type
- protein
- Length
- 3,468 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinate-nucleotide pyrophosphorylase [carboxylating]
- EC
- 2.4.2.19
- UniProt
- V9HWJ5
- Ligands
- NCN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Nicotinate-nucleotide pyrophosphorylase [carboxylating] (EC 2.4.2.19) | protein | 289 | 44% helix, 19% strand | V9HWJ5 |
Ligands and binding sites
- NCN · Nicotinate mononucleotide · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 745 | 0.85 | 0.88 | 91 | NCN |
| 2 | 1078 | 0.85 | 0.86 | 138 | empty |
| 3 | 1103 | 0.82 | 0.83 | 107 | empty |
| 4 | 271 | 0.79 | 0.91 | 49 | NCN |
| 5 | 109 | 0.75 | 0.95 | 23 | empty |
Interfaces
33 interfaces between chains.
- I–J · 2554 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 2546 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 2545 Ų buried · 39 hydrogen bonds · protein-protein
- G–H · 2543 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 2538 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 5AYZ · Crystal structure of human quinolinate phosphoribosyltransferase in complex with the… · 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 V9HWJ5
- Elsewhere: RCSB PDB 5AYZ · PDBe 5AYZ · UniProt V9HWJ5
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