MolNFT v1 · #21937 · protein
Crystal structure of E. COLI pantothenate kinase
1SQ5: “Crystal structure of E. COLI pantothenate kinase”. X-ray diffraction, 2 ligands (PAU, ADP), 8 pockets (best druggability 0.86). MolNFT v1 #21937 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1SQ5
- Type
- protein
- Length
- 1,206 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
- PAU, ADP
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pantothenate kinase (EC 2.7.1.33) | protein | 302 | 49% helix, 17% strand | P0A6I3 |
| B | Pantothenate kinase (EC 2.7.1.33) | protein | 302 | 48% helix, 18% strand | P0A6I3 |
| C | Pantothenate kinase (EC 2.7.1.33) | protein | 298 | 50% helix, 17% strand | P0A6I3 |
| D | Pantothenate kinase (EC 2.7.1.33) | protein | 304 | 49% helix, 17% strand | P0A6I3 |
Ligands and binding sites
- PAU · Pantothenoic acid · ligand · 4 copies · chains A, B, C, D
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.86 | 0.88 | 83 | empty |
| 2 | 782 | 0.77 | 0.81 | 74 | PAU, ADP |
| 3 | 667 | 0.77 | 0.82 | 75 | PAU, ADP |
| 4 | 601 | 0.76 | 0.83 | 59 | PAU, ADP |
| 5 | 599 | 0.76 | 0.82 | 60 | PAU, ADP |
Interfaces
4 interfaces between chains.
- A–D · 1954 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 362 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 361 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 16 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 1SQ5 · PDBe 1SQ5 · UniProt P0A6I3
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