MolNFT v1 · #169792 · protein
Crystal structure of 2-hydroxyacyl CoA lyase (hacl) from rhodospirillales bacterium URHD0017
6XN8 · 2-hydroxyacyl-CoA lyase 1: “Crystal structure of 2-hydroxyacyl CoA lyase (hacl) from rhodospirillales bacterium URHD0017”. X-ray diffraction, 4 ligands (TZD, ADP, UNL), 8 pockets (best druggability 0.79). MolNFT v1 #169792 on…
- PDB
- 6XN8
- Type
- protein
- Length
- 1,079 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-hydroxyacyl-CoA lyase 1
- UniProt
- A0A1H8YFL8
- Ligands
- TZD, ADP, UNL, MG
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-hydroxyacyl-CoA lyase 1 | protein | 540 | 44% helix, 18% strand | A0A1H8YFL8 |
| B | 2-hydroxyacyl-CoA lyase 1 | protein | 539 | 44% helix, 18% strand | A0A1H8YFL8 |
Ligands and binding sites
- TZD · 2-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-4-methyl-2-oxo-2,3-dihydro-1,3-thiazol-5-yl}ethyl trihydrogen diphosphate · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- UNL · Unknown ligand · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 885 | 0.79 | 0.82 | 115 | MG, TZD, ADP |
| 2 | 925 | 0.79 | 0.81 | 117 | MG, TZD, ADP |
| 3 | 183 | 0.49 | 0.77 | 26 | empty |
| 4 | 191 | 0.49 | 0.76 | 27 | empty |
| 5 | 71 | 0.44 | 0.81 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 3389 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 6XN8 · Crystal Structure of 2-hydroxyacyl CoA lyase (HACL) from Rhodospirillales bacterium… · 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 A0A1H8YFL8
- Elsewhere: RCSB PDB 6XN8 · PDBe 6XN8 · UniProt A0A1H8YFL8
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