MolNFT v1 · #24856 · protein
Crystal structure of pantoate-beta-alanine (pantothenate synthetase) from thermus thermophilus HB8
1V8F · Pantoate-beta-alanine ligase: “Crystal structure of pantoate-beta-alanine (pantothenate synthetase) from thermus thermophilus HB8”. X-ray diffraction, 1 ligand (CL), 7 pockets (best druggability 0.85). MolNFT v1 #24856 on GenesisL1…
- PDB
- 1V8F
- Type
- protein
- Length
- 552 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pantoate-beta-alanine ligase
- EC
- 6.3.2.1
- UniProt
- P83701
- Ligands
- CL
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pantoate-beta-alanine ligase (EC 6.3.2.1) | protein | 276 | 42% helix, 22% strand | P83701 |
Ligands and binding sites
- CL · Chloride ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
- 144 · Tris-hydroxymethyl-methyl-ammonium · additive · chains A
- P6G · Hexaethylene glycol · additive · chains A
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 | 458 | 0.85 | 0.92 | 71 | CL, 144, GOL |
| 2 | 473 | 0.83 | 0.90 | 72 | CL, GOL |
| 3 | 249 | 0.54 | 0.77 | 32 | empty |
| 4 | 52 | 0.34 | 0.78 | 16 | empty |
| 5 | 58 | 0.33 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1174 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1V8F · Crystal Structure of Pantoate-beta-Alanine (Pantothenate Synthetase) from Thermus… · 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 P83701
- Elsewhere: RCSB PDB 1V8F · PDBe 1V8F · UniProt P83701
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