Research workbench
Pyrobaculum calidifontis 5-aminolaevulinic acid dehydratase
Analyse Pyrobaculum calidifontis 5-aminolaevulinic acid dehydratase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LZL
- Type
- protein
- Length
- 4,032 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Delta-aminolevulinic acid dehydratase
- EC
- 4.2.1.24
- UniProt
- A3MWV9
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) | protein | 336 | 40% helix, 16% strand | A3MWV9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
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 | 1179 | 0.82 | 0.83 | 93 | empty |
| 2 | 1162 | 0.82 | 0.83 | 82 | empty |
| 3 | 1136 | 0.82 | 0.83 | 86 | empty |
| 4 | 1110 | 0.81 | 0.83 | 78 | empty |
| 5 | 661 | 0.77 | 0.82 | 44 | empty |
Interfaces
26 interfaces between chains.
- C–E · 3786 Ų buried · 70 hydrogen bonds · protein-protein
- B–H · 3783 Ų buried · 76 hydrogen bonds · protein-protein
- A–G · 3779 Ų buried · 62 hydrogen bonds · protein-protein
- D–F · 3753 Ų buried · 67 hydrogen bonds · protein-protein
- B–F · 1766 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5LZL · Pyrobaculum calidifontis 5-aminolaevulinic acid dehydratase · the same entry in another collection · chain A 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 A3MWV9
- Elsewhere: RCSB PDB 5LZL · PDBe 5LZL · UniProt A3MWV9
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