Research workbench
Crystal structure of pantoate-beta-alanine-ligase in complex with ATP at low occupancy at 2.1 a resolution
Analyse Crystal structure of pantoate-beta-alanine-ligase in complex with ATP at low… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3INN
- Type
- protein
- Length
- 1,122 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pantothenate synthetase
- EC
- 6.3.2.1
- UniProt
- Q8YFC9
- Ligands
- ATP, UNX
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pantothenate synthetase (EC 6.3.2.1) | protein | 283 | 41% helix, 21% strand | Q8YFC9 |
| B | Pantothenate synthetase (EC 6.3.2.1) | protein | 278 | 41% helix, 22% strand | Q8YFC9 |
| C | Pantothenate synthetase (EC 6.3.2.1) | protein | 284 | 42% helix, 21% strand | Q8YFC9 |
| D | Pantothenate synthetase (EC 6.3.2.1) | protein | 277 | 40% helix, 22% strand | Q8YFC9 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, C, D
- UNX · Unknown atom or ion · ion · 6 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.85 | 0.94 | 57 | ATP, UNX |
| 2 | 1012 | 0.85 | 0.86 | 102 | empty |
| 3 | 323 | 0.84 | 0.94 | 54 | ATP, UNX |
| 4 | 549 | 0.76 | 0.83 | 54 | empty |
| 5 | 481 | 0.75 | 0.83 | 52 | ATP |
Interfaces
6 interfaces between chains.
- A–D · 1243 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1202 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 719 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 716 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 135 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3INN · Crystal structure of pantoate-beta-alanine-ligase in complex with ATP at low occupancy at… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8YFC9 · AlphaFold monomer V2.0 prediction for pantothenate synthetase (Q8YFC9) · 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 Q8YFC9
- Elsewhere: RCSB PDB 3INN · PDBe 3INN · UniProt Q8YFC9
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