Research workbench
Crystal structure of mycobacterium tuberculosis pnp with transition state analog dadme-immh
Analyse Crystal structure of mycobacterium tuberculosis pnp with transition state… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N3I
- Type
- protein
- Length
- 786 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- P0A538
- Ligands
- DIH, PO4
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 262 | 35% helix, 24% strand | P0A538 |
Ligands and binding sites
- DIH · 7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.85 | 0.95 | 47 | empty |
| 2 | 110 | 0.79 | 0.98 | 27 | PO4, DIH |
| 3 | 115 | 0.79 | 0.97 | 26 | PO4, DIH |
| 4 | 115 | 0.78 | 0.97 | 26 | PO4, DIH |
| 5 | 658 | 0.69 | 0.77 | 109 | empty |
Interfaces
3 interfaces between chains.
- A–C · 922 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 909 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 903 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1N3I · Crystal Structure of Mycobacterium tuberculosis PNP with transition state analog… · the same entry in another collection · chain C against C, 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 1N3I · PDBe 1N3I · UniProt P0A538
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