Research workbench
Structural basis for the feedback regulation of escherichia COLI pantothenate kinase by coenzyme a
Analyse Structural basis for the feedback regulation of escherichia COLI pantothenate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ESM
- Type
- protein
- Length
- 1,228 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pantothenate kinase
- EC
- 2.7.1.33
- UniProt
- P0A6I3
- Ligands
- COA
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pantothenate kinase (EC 2.7.1.33) | protein | 311 | 46% helix, 16% strand | P0A6I3 |
| B | Pantothenate kinase (EC 2.7.1.33) | protein | 307 | 44% helix, 16% strand | P0A6I3 |
| C | Pantothenate kinase (EC 2.7.1.33) | protein | 307 | 46% helix, 17% strand | P0A6I3 |
| D | Pantothenate kinase (EC 2.7.1.33) | protein | 303 | 44% helix, 17% strand | P0A6I3 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 777 | 0.83 | 0.85 | 77 | COA |
| 2 | 844 | 0.81 | 0.83 | 78 | empty |
| 3 | 518 | 0.79 | 0.86 | 45 | empty |
| 4 | 486 | 0.78 | 0.85 | 42 | COA |
| 5 | 540 | 0.78 | 0.84 | 54 | COA |
Interfaces
5 interfaces between chains.
- A–B · 1699 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1698 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 525 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 281 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 148 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 1ESM · Structural basis for the feedback regulation of escherichia COLI pantothenate kinase by… · the same entry in another collection · chain D against D, TM-score 1.00
- P0A6I3 · AlphaFold monomer V2.0 prediction for pantothenate kinase (P0A6I3) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 P0A6I3
- Elsewhere: RCSB PDB 1ESM · PDBe 1ESM · UniProt P0A6I3
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