MolNFT v1 · #32646 · protein
5-aminolevulinate synthase from rhodobacter capsulatus
2BWN: “5-aminolevulinate synthase from rhodobacter capsulatus”. X-ray diffraction, 3 ligands (PLP, CL, SO4), 13 pockets (best druggability 0.81). MolNFT v1 #32646 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2BWN
- Type
- protein
- Length
- 1,586 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
- PLP, CL, SO4
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-aminolevulinate synthase (EC 2.3.1.37) | protein | 396 | 45% helix, 17% strand | P18079 |
| B | 5-aminolevulinate synthase (EC 2.3.1.37) | protein | 395 | 44% helix, 18% strand | P18079 |
| D | 5-aminolevulinate synthase (EC 2.3.1.37) | protein | 397 | 45% helix, 17% strand | P18079 |
| E | 5-aminolevulinate synthase (EC 2.3.1.37) | protein | 398 | 45% helix, 17% strand | P18079 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, D, E
- CL · Chloride ion · ion · 2 copies · chains A, E
- SO4 · Sulfate ion · ion · chains A, B
- SIN · Succinic acid · additive · 3 copies · chains A, D, E
- ACY · Acetic acid · additive · 2 copies · chains A, B, D, E
- FMT · Formic acid · additive · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.81 | 0.87 | 81 | PLP, SO4 |
| 2 | 464 | 0.76 | 0.84 | 65 | FMT |
| 3 | 91 | 0.73 | 0.96 | 32 | empty |
| 4 | 739 | 0.73 | 0.79 | 75 | ACY |
| 5 | 293 | 0.71 | 0.85 | 52 | ACY |
Interfaces
6 interfaces between chains.
- D–E · 4500 Ų buried · 71 hydrogen bonds · protein-protein
- A–B · 4393 Ų buried · 70 hydrogen bonds · protein-protein
- B–D · 567 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 98 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 18 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
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 P18079
- Elsewhere: RCSB PDB 2BWN · PDBe 2BWN · UniProt P18079
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