Research workbench
Crystal structure of 3-ketoacyl-CoA thiolase (mmga) from bacillus subtilis.
Analyse Crystal structure of 3-ketoacyl-CoA thiolase (mmga) from bacillus subtilis. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LP7
- Type
- protein
- Length
- 3,084 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyl-CoA acetyltransferase
- EC
- 2.3.1.9
- UniProt
- P45855
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 8 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 386 | 37% helix, 23% strand | P45855 |
| E | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 386 | 37% helix, 24% strand | P45855 |
| A | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 386 | 38% helix, 23% strand | P45855 |
| B | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 388 | 38% helix, 23% strand | P45855 |
| C | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 387 | 37% helix, 23% strand | P45855 |
| F | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 380 | 37% helix, 22% strand | P45855 |
| G | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 385 | 37% helix, 21% strand | P45855 |
| D | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 386 | 37% helix, 23% strand | P45855 |
Ligands and binding sites
- GOL · Glycerol · additive · 8 copies · chains H, E, A, B, C, D, F, G
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 | 425 | 0.76 | 0.85 | 64 | empty |
| 2 | 62 | 0.69 | 0.96 | 22 | empty |
| 3 | 241 | 0.66 | 0.83 | 37 | GOL |
| 4 | 227 | 0.65 | 0.83 | 41 | empty |
| 5 | 255 | 0.64 | 0.82 | 43 | empty |
Interfaces
13 interfaces between chains.
- A–B · 2622 Ų buried · 59 hydrogen bonds · protein-protein
- H–G · 2594 Ų buried · 55 hydrogen bonds · protein-protein
- E–F · 2585 Ų buried · 59 hydrogen bonds · protein-protein
- C–D · 2541 Ų buried · 57 hydrogen bonds · protein-protein
- A–D · 715 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5LP7 · Crystal structure of 3-Ketoacyl-CoA Thiolase (MmgA) from Bacillus subtilis. · the same entry in another collection · chain D against D, TM-score 1.00
- P45855 · AlphaFold monomer V2.0 prediction for acetyl-CoA acetyltransferase (P45855) · a predicted model of the same protein · chain H against A, TM-score 1.00
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 P45855
- Elsewhere: RCSB PDB 5LP7 · PDBe 5LP7 · UniProt P45855
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