MolNFT v1 · #188370 · protein
Crystal structure of pantothenate synthetase from bartonella henselae
7TOT: “Crystal structure of pantothenate synthetase from bartonella henselae”. X-ray diffraction, 2 ligands (NO3, SO4), 7 pockets (best druggability 0.72). MolNFT v1 #188370 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7TOT
- 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
- Q6G456
- Ligands
- NO3, SO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pantothenate synthetase (EC 6.3.2.1) | protein | 283 | 42% helix, 23% strand | Q6G456 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · 7 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 557 | 0.72 | 0.80 | 57 | MPD |
| 2 | 532 | 0.71 | 0.80 | 60 | MPD, NO3 |
| 3 | 223 | 0.54 | 0.78 | 30 | NO3 |
| 4 | 91 | 0.50 | 0.82 | 18 | empty |
| 5 | 114 | 0.44 | 0.78 | 19 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1268 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 7TOT · Crystal Structure of pantothenate synthetase from Bartonella henselae · the same entry in another collection · chain A against A, TM-score 1.00
- Q6G456 · AlphaFold monomer V2.0 prediction for pantothenate synthetase (Q6G456) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 Q6G456
- Elsewhere: RCSB PDB 7TOT · PDBe 7TOT · UniProt Q6G456
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