MolNFT v1 · #140557 · protein
Mechanistic insight into the regulation of pseudomonas aeruginosa aspartate kinase
5YEI · Aspartokinase: “Mechanistic insight into the regulation of pseudomonas aeruginosa aspartate kinase”. X-ray diffraction, 2 ligands (THR, LYS), 20 pockets (best druggability 0.82). MolNFT v1 #140557 on GenesisL1: 3D structure, binding…
- PDB
- 5YEI
- Type
- protein
- Length
- 2,207 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartokinase
- EC
- 2.7.2.4
- UniProt
- O69077
- Ligands
- THR, LYS
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, B, H | Aspartokinase (EC 2.7.2.4) | protein | 156 | 38% helix, 34% strand | O69077 |
| F | Aspartokinase (EC 2.7.2.4) | protein | 151 | 40% helix, 32% strand | O69077 |
| C, G, A, E | Aspartokinase (EC 2.7.2.4) | protein | 397 | 37% helix, 26% strand | O69077 |
Ligands and binding sites
- THR · Threonine · ligand · 8 copies · chains D, C, B, A, F, E, H, G
- LYS · Lysine · ligand · 4 copies · chains D, C, H, G, B, A, F, E
- GOL · Glycerol · additive · 3 copies · chains G, A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 963 | 0.82 | 0.84 | 104 | empty |
| 2 | 983 | 0.78 | 0.80 | 90 | LYS |
| 3 | 800 | 0.76 | 0.80 | 82 | LYS |
| 4 | 1112 | 0.76 | 0.78 | 104 | empty |
| 5 | 754 | 0.75 | 0.80 | 81 | LYS |
Interfaces
14 interfaces between chains.
- B–A · 2454 Ų buried · 45 hydrogen bonds · protein-protein
- D–C · 2450 Ų buried · 47 hydrogen bonds · protein-protein
- H–G · 2408 Ų buried · 40 hydrogen bonds · protein-protein
- F–E · 2379 Ų buried · 37 hydrogen bonds · protein-protein
- G–E · 1608 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5YEI · Mechanistic insight into the regulation of Pseudomonas aeruginosa aspartate kinase · the same entry in another collection · chain E against E, TM-score 1.00
- O69077 · AlphaFold monomer V2.0 prediction for aspartokinase (O69077) · a predicted model of the same protein · chain F 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 O69077
- Elsewhere: RCSB PDB 5YEI · PDBe 5YEI · UniProt O69077
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