Research workbench
5-aminolevulinate synthase from rhodobacter capsulatus in complex with succinyl-CoA
Analyse 5-aminolevulinate synthase from rhodobacter capsulatus in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BWO
- Type
- protein
- Length
- 1,593 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-aminolevulinate synthase
- EC
- 2.3.1.37
- UniProt
- P18079
- Ligands
- SCA, PLP
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-aminolevulinate synthase (EC 2.3.1.37) | protein | 398 | 44% helix, 17% strand | P18079 |
| B, E | 5-aminolevulinate synthase (EC 2.3.1.37) | protein | 399 | 44% helix, 17% strand | P18079 |
| D | 5-aminolevulinate synthase (EC 2.3.1.37) | protein | 397 | 44% helix, 17% strand | P18079 |
Ligands and binding sites
- SCA · Succinyl-coenzyme A · ligand · 4 copies · chains A, B, E, D
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.81 | 0.86 | 102 | SCA, PLP |
| 2 | 342 | 0.77 | 0.87 | 61 | SCA, PLP |
| 3 | 444 | 0.75 | 0.84 | 71 | SCA, PLP |
| 4 | 107 | 0.64 | 0.89 | 27 | empty |
| 5 | 141 | 0.50 | 0.79 | 18 | empty |
Interfaces
6 interfaces between chains.
- D–E · 4586 Ų buried · 70 hydrogen bonds · protein-protein
- A–B · 4552 Ų buried · 68 hydrogen bonds · protein-protein
- B–D · 384 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 68 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 22 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2BWO · 5-Aminolevulinate Synthase from Rhodobacter capsulatus in complex with succinyl-CoA · the same entry in another collection · chain A against A, TM-score 1.00
- P18079 · AlphaFold monomer V2.0 prediction for 5-aminolevulinate synthase (P18079) · a predicted model of the same protein · chain D 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 P18079
- Elsewhere: RCSB PDB 2BWO · PDBe 2BWO · UniProt P18079
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.