Research workbench
Qprtase structure from human
Analyse Qprtase structure from human in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JBM
- Type
- protein
- Length
- 3,434 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinate-nucleotide pyrophosphorylase
- EC
- 2.4.2.19
- UniProt
- Q15274
- Ligands
- SRT
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinate-nucleotide pyrophosphorylase (EC 2.4.2.19) | protein | 289 | 45% helix, 20% strand | Q15274 |
| B, E, I | Nicotinate-nucleotide pyrophosphorylase (EC 2.4.2.19) | protein | 288 | 45% helix, 20% strand | Q15274 |
| C | Nicotinate-nucleotide pyrophosphorylase (EC 2.4.2.19) | protein | 286 | 45% helix, 19% strand | Q15274 |
| D, F, G, H, J, K, L | Nicotinate-nucleotide pyrophosphorylase (EC 2.4.2.19) | protein | 285 | 46% helix, 19% strand | Q15274 |
Ligands and binding sites
- SRT · S,R meso-tartaric acid · 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 | 1015 | 0.87 | 0.87 | 144 | empty |
| 2 | 1040 | 0.86 | 0.87 | 143 | empty |
| 3 | 1133 | 0.82 | 0.83 | 178 | SRT |
| 4 | 764 | 0.79 | 0.83 | 122 | SRT |
| 5 | 377 | 0.75 | 0.85 | 53 | SRT |
Interfaces
31 interfaces between chains.
- A–B · 2576 Ų buried · 45 hydrogen bonds · protein-protein
- E–F · 2566 Ų buried · 40 hydrogen bonds · protein-protein
- K–L · 2543 Ų buried · 44 hydrogen bonds · protein-protein
- G–H · 2533 Ų buried · 43 hydrogen bonds · protein-protein
- I–J · 2511 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 2JBM · Qprtase structure from human · the same entry in another collection · chain L against L, 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 Q15274
- Elsewhere: RCSB PDB 2JBM · PDBe 2JBM · UniProt Q15274
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