Research workbench
Crystal structure of S. aureus pyruvate kinase in complex with a naturally occurring bis-indole alkaloid
Analyse Crystal structure of S. aureus pyruvate kinase in complex with a naturally… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T07
- 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
- 09C, PO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyruvate kinase (EC 2.7.1.40) | protein | 583 | 35% helix, 22% strand | Q6GG09 |
Ligands and binding sites
- 09C · (3S,5R)-3,5-bis(6-bromo-1H-indol-3-yl)piperazin-2-one · ligand · 2 copies · chains A, B, C, D
- 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 936 | 0.78 | 0.80 | 83 | empty |
| 2 | 1146 | 0.78 | 0.80 | 101 | PO4 |
| 3 | 1099 | 0.77 | 0.79 | 84 | empty |
| 4 | 784 | 0.77 | 0.81 | 38 | empty |
| 5 | 807 | 0.77 | 0.81 | 38 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1912 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1905 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 1258 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1233 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3T07 · Crystal structure of S. aureus Pyruvate Kinase in complex with a naturally occurring… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6GG09 · AlphaFold monomer V2.0 prediction for pyruvate kinase (Q6GG09) · a predicted model of the same protein · chain A 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 Q6GG09
- Elsewhere: RCSB PDB 3T07 · PDBe 3T07 · UniProt Q6GG09
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