Research workbench
Pantothenate synthetase in complex with racemate (2S)-2,3-dihydro-1,4- benzodioxine-2-carboxylic acid and (2R)-2,3-dihydro-1,4-benzodioxine- 2-carboxylic acid
Analyse Pantothenate synthetase in complex with racemate (2S)-2,3-dihydro-1,4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G5F
- Type
- protein
- Length
- 554 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
- 0JD, 15N
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pantothenate synthetase (EC 6.3.2.1) | protein | 282 | 40% helix, 23% strand | P0A5R0 |
| B | Pantothenate synthetase (EC 6.3.2.1) | protein | 272 | 42% helix, 24% strand | P0A5R0 |
Ligands and binding sites
- 0JD · (2S)-2,3-dihydro-1,4-benzodioxine-2-carboxylic acid · ligand · 2 copies · chains A, B
- 15N · (2R)-2,3-dihydro-1,4-benzodioxine-2-carboxylic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- EOH · Ethanol · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · 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 | 497 | 0.83 | 0.89 | 59 | 0JD, 15N |
| 2 | 462 | 0.79 | 0.87 | 54 | 15N, 0JD |
| 3 | 347 | 0.64 | 0.79 | 34 | EOH |
| 4 | 65 | 0.31 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1174 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4G5F · Pantothenate synthetase in complex with racemate… · 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 4G5F · PDBe 4G5F · UniProt P0A5R0
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