MolNFT v1 · #67573 · protein
Crystal structure of mycobacterium tuberculosis pantothenate synthetase at 2.50 ang resolution in complex with 5'-deoxy-5'- (benzyldisulfanyl)-adenosine
3IOC: “Crystal structure of mycobacterium tuberculosis pantothenate synthetase at 2.50 ang resolution in complex…”. X-ray diffraction, 1 ligand (A5D), 3 pockets (best druggability 0.79). MolNFT v1 #67573 on GenesisL1: 3D structure, binding…
- PDB
- 3IOC
- Type
- protein
- Length
- 547 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pantothenate synthetase
- EC
- 6.3.2.1
- UniProt
- P0A5R0
- Ligands
- A5D
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pantothenate synthetase (EC 6.3.2.1) | protein | 273 | 42% helix, 23% strand | P0A5R0 |
| B | Pantothenate synthetase (EC 6.3.2.1) | protein | 274 | 42% helix, 24% strand | P0A5R0 |
Ligands and binding sites
- A5D · (2R,3R,4S,5S)-2-(6-amino-9H-purin-9-yl)-5-[(benzyldisulfanyl)methyl]tetrahydrofuran-3,4-diol · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 480 | 0.79 | 0.86 | 53 | A5D |
| 2 | 436 | 0.77 | 0.85 | 54 | A5D |
| 3 | 317 | 0.62 | 0.79 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1207 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 3IOC · Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 2.50 Ang… · 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 P0A5R0
- Elsewhere: RCSB PDB 3IOC · PDBe 3IOC · UniProt P0A5R0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.