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Crystal structure of mycobacterium tuberculosis pantothenate synthetase in complex with fragment 1
Analyse Crystal structure of mycobacterium tuberculosis pantothenate synthetase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EF6
- 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
- I2E
- Pockets
- 4 · best druggability 0.83
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 | 290 | 42% helix, 22% strand | P0A5R0 |
| B | Pantothenate synthetase (EC 6.3.2.1) | protein | 276 | 41% helix, 24% strand | P0A5R0 |
Ligands and binding sites
- I2E · 3-(1,3-benzodioxol-5-yl)propanoic acid · ligand · 2 copies · chains A, B
- EOH · Ethanol · additive · 5 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 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 | 527 | 0.83 | 0.89 | 64 | I2E, EDO |
| 2 | 436 | 0.77 | 0.86 | 50 | GOL, I2E |
| 3 | 303 | 0.55 | 0.76 | 33 | EOH, GOL |
| 4 | 69 | 0.32 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1187 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 4EF6 · Crystal Structure of Mycobacterium tuberculosis Pantothenate synthetase in complex with… · 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 4EF6 · PDBe 4EF6 · UniProt P0A5R0
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