MolNFT v1 · #67574 · protein
Crystal structure of mycobacterium tuberculosis pantothenate synthetase at 1.75 ang resolution in complex with 5'-deoxy-5'-((3- NITROBENZYL)DISULFANYL)-adenosine
3IOD: “Crystal structure of mycobacterium tuberculosis pantothenate synthetase at 1.75 ang resolution in complex…”. X-ray diffraction, 2 ligands (A6D, SO4), 4 pockets (best druggability 0.81). MolNFT v1 #67574 on GenesisL1: 3D structure…
- PDB
- 3IOD
- Type
- protein
- Length
- 548 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
- A6D, SO4
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pantothenate synthetase (EC 6.3.2.1) | protein | 276 | 42% helix, 23% strand | P0A5R0 |
| B | Pantothenate synthetase (EC 6.3.2.1) | protein | 272 | 42% helix, 25% strand | P0A5R0 |
Ligands and binding sites
- A6D · (2R,3R,4S,5S)-2-(6-amino-9H-purin-9-yl)-5-{[(3-nitrobenzyl)disulfanyl]methyl}tetrahydrofuran-3,4-diol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EOH · Ethanol · additive · 3 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
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.81 | 0.88 | 59 | A6D, SO4 |
| 2 | 469 | 0.78 | 0.86 | 53 | A6D, SO4 |
| 3 | 344 | 0.67 | 0.81 | 32 | empty |
| 4 | 54 | 0.31 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1194 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 3IOD · Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 1.75 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 3IOD · PDBe 3IOD · UniProt P0A5R0
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