Research workbench
Pantothenate synthetase in complex with fragment 6
Analyse Pantothenate synthetase in complex with fragment 6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DE5
- Type
- protein
- Length
- 565 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
- Pockets
- 4 · 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 | 289 | 42% helix, 22% strand | P0A5R0 |
| B | Pantothenate synthetase (EC 6.3.2.1) | protein | 276 | 43% 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
- GOL · Glycerol · additive · 2 copies · chains A, B
- EOH · Ethanol · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · 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 | 492 | 0.84 | 0.91 | 66 | 0JD |
| 2 | 453 | 0.80 | 0.88 | 56 | 0JD |
| 3 | 339 | 0.68 | 0.82 | 32 | EOH |
| 4 | 66 | 0.33 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1221 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 4DE5 · Pantothenate synthetase in complex with fragment 6 · 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 4DE5 · PDBe 4DE5 · UniProt P0A5R0
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