Research workbench
Crystal structure of 4-phosphopantoate-beta-alanine ligase from thermococcus kodakarensis
Analyse Crystal structure of 4-phosphopantoate-beta-alanine ligase from thermococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WDM
- Type
- protein
- Length
- 1,028 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
- ADN
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-phosphopantoate--beta-alanine ligase (EC 6.3.2.36) | protein | 259 | 55% helix, 9% strand | Q5JIZ8 |
| B | 4-phosphopantoate--beta-alanine ligase (EC 6.3.2.36) | protein | 256 | 53% helix, 11% strand | Q5JIZ8 |
| C | 4-phosphopantoate--beta-alanine ligase (EC 6.3.2.36) | protein | 258 | 56% helix, 10% strand | Q5JIZ8 |
| D | 4-phosphopantoate--beta-alanine ligase (EC 6.3.2.36) | protein | 255 | 51% helix, 12% strand | Q5JIZ8 |
Ligands and binding sites
- ADN · Adenosine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.82 | 0.88 | 78 | ADN |
| 2 | 433 | 0.79 | 0.87 | 60 | ADN |
| 3 | 683 | 0.79 | 0.83 | 75 | ADN |
| 4 | 574 | 0.76 | 0.83 | 67 | ADN |
| 5 | 74 | 0.57 | 0.88 | 20 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1906 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1870 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 405 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 400 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 355 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3WDM · Crystal structure of 4-phosphopantoate-beta-alanine ligase from Thermococcus kodakarensis · 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 A 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 3WDM · PDBe 3WDM · UniProt Q5JIZ8
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