Research workbench
Crystal structure of 4-phosphopantoate-beta-alanine ligase complexed with ATP
Analyse Crystal structure of 4-phosphopantoate-beta-alanine ligase complexed with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WDL
- Type
- protein
- Length
- 1,013 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-phosphopantoate--beta-alanine ligase
- EC
- 6.3.2.36
- UniProt
- Q5JIZ8
- Ligands
- ATP, MG
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-phosphopantoate--beta-alanine ligase (EC 6.3.2.36) | protein | 257 | 55% helix, 9% strand | Q5JIZ8 |
| B | 4-phosphopantoate--beta-alanine ligase (EC 6.3.2.36) | protein | 253 | 55% helix, 10% strand | Q5JIZ8 |
| C | 4-phosphopantoate--beta-alanine ligase (EC 6.3.2.36) | protein | 254 | 56% helix, 10% strand | Q5JIZ8 |
| D | 4-phosphopantoate--beta-alanine ligase (EC 6.3.2.36) | protein | 249 | 52% helix, 10% strand | Q5JIZ8 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1055 | 0.86 | 0.87 | 127 | ATP, MG |
| 2 | 505 | 0.78 | 0.85 | 54 | ATP, MG |
| 3 | 619 | 0.72 | 0.79 | 55 | ATP |
| 4 | 470 | 0.69 | 0.80 | 51 | empty |
| 5 | 96 | 0.55 | 0.85 | 20 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1933 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1891 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 540 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 244 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3WDL · Crystal structure of 4-phosphopantoate-beta-alanine ligase complexed with ATP · the same entry in another collection · chain D against D, TM-score 1.00
- Q5JIZ8 · AlphaFold monomer V2.0 prediction for 4-phosphopantoate--beta-alanine ligase (Q5JIZ8) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q5JIZ8
- Elsewhere: RCSB PDB 3WDL · PDBe 3WDL · UniProt Q5JIZ8
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