MolNFT v1 · #30737 · protein
Crystal structure of a pantothenate synthetase complexed with AMP and beta-alanine
2A86 · Pantoate--beta-alanine ligase: “Crystal structure of a pantothenate synthetase complexed with AMP and beta-alanine”. X-ray diffraction, 3 ligands (AMP, BAL, SO4), 7 pockets (best druggability 0.84). MolNFT v1 #30737 on GenesisL1: 3D…
- PDB
- 2A86
- Type
- protein
- Length
- 565 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
- P0A5R0
- Ligands
- AMP, BAL, SO4
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pantoate--beta-alanine ligase (EC 6.3.2.1) | protein | 288 | 43% helix, 23% strand | P0A5R0 |
| B | Pantoate--beta-alanine ligase (EC 6.3.2.1) | protein | 277 | 44% helix, 24% strand | P0A5R0 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- BAL · Beta-alanine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 5 copies · chains A, B
- EOH · Ethanol · additive · 5 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 | 468 | 0.84 | 0.91 | 55 | AMP, BAL, GOL |
| 2 | 531 | 0.78 | 0.85 | 60 | AMP, GOL, EOH |
| 3 | 264 | 0.63 | 0.81 | 22 | EOH |
| 4 | 56 | 0.34 | 0.78 | 11 | empty |
| 5 | 65 | 0.33 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1233 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 2A86 · Crystal structure of A Pantothenate synthetase complexed with AMP and beta-alanine · 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 2A86 · PDBe 2A86 · UniProt P0A5R0
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