MolNFT v1 · #67575 · protein
Crystal structure of mycobacterium tuberculosis pantothenate synthetase at 1.95 ang resolution in complex with 5'-deoxy-5'-((R)-3, 4-dihydroxybutylthio)-adenosine
3IOE: “Crystal structure of mycobacterium tuberculosis pantothenate synthetase at 1.95 ang resolution in complex…”. X-ray diffraction, 2 ligands (A7D, SO4), 5 pockets (best druggability 0.84). MolNFT v1 #67575 on GenesisL1: 3D structure…
- PDB
- 3IOE
- Type
- protein
- Length
- 566 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
- A7D, SO4
- Pockets
- 5 · best druggability 0.84
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 | 286 | 42% helix, 22% strand | P0A5R0 |
| B | Pantothenate synthetase (EC 6.3.2.1) | protein | 280 | 42% helix, 24% strand | P0A5R0 |
Ligands and binding sites
- A7D · 5'-S-[(3R)-3,4-dihydroxybutyl]-5'-thioadenosine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- EOH · Ethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 534 | 0.84 | 0.90 | 62 | A7D, SO4 |
| 2 | 460 | 0.82 | 0.89 | 52 | A7D, SO4 |
| 3 | 338 | 0.66 | 0.81 | 33 | empty |
| 4 | 64 | 0.32 | 0.76 | 15 | empty |
| 5 | 58 | 0.31 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1199 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3IOE · Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 1.95 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 3IOE · PDBe 3IOE · UniProt P0A5R0
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