MolNFT v1 · #79334 · protein
Crystal structure of S. aureus pyruvate kinase
3T05: “Crystal structure of S. aureus pyruvate kinase”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.78). MolNFT v1 #79334 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3T05
- Type
- protein
- Length
- 2,332 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase
- EC
- 2.7.1.40
- UniProt
- Q6GG09
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyruvate kinase (EC 2.7.1.40) | protein | 583 | 36% helix, 24% strand | Q6GG09 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.78 | 0.80 | 75 | empty |
| 2 | 671 | 0.78 | 0.83 | 54 | empty |
| 3 | 630 | 0.77 | 0.83 | 50 | empty |
| 4 | 1181 | 0.76 | 0.79 | 82 | empty |
| 5 | 1179 | 0.76 | 0.78 | 80 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1849 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1843 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1193 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1173 Ų buried · 16 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 Q6GG09
- Elsewhere: RCSB PDB 3T05 · PDBe 3T05 · UniProt Q6GG09
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