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Combining crystallographic, thermodynamic, and molecular dynamics studies of mycobacterium tuberculosis purine nucleoside phosphorylase
Analyse Combining crystallographic, thermodynamic, and molecular dynamics studies of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SCZ
- Type
- protein
- Length
- 525 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- P0A538
- Ligands
- HPA
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 263 | 37% helix, 24% strand | P0A538 |
| B | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 262 | 36% helix, 24% strand | P0A538 |
Ligands and binding sites
- HPA · Hypoxanthine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.65 | 0.90 | 23 | HPA |
| 2 | 113 | 0.61 | 0.87 | 25 | HPA |
| 3 | 166 | 0.58 | 0.82 | 30 | empty |
| 4 | 75 | 0.42 | 0.80 | 21 | empty |
| 5 | 109 | 0.40 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 587 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3SCZ · Combining crystallographic, thermodynamic, and molecular dynamics studies of… · 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 P0A538
- Elsewhere: RCSB PDB 3SCZ · PDBe 3SCZ · UniProt P0A538
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