MolNFT v1 · #77269 · protein
Structure of a carnitinyl-CoA dehydratase from mycobacterium avium 104
3R9S: “Structure of a carnitinyl-CoA dehydratase from mycobacterium avium 104”. X-ray diffraction, 1 ligand (BEZ), 7 pockets (best druggability 0.81). MolNFT v1 #77269 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3R9S
- Type
- protein
- Length
- 772 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carnitinyl-CoA dehydratase
- EC
- 4.2.1.-
- UniProt
- A0QC84
- Ligands
- BEZ
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carnitinyl-CoA dehydratase (EC 4.2.1.-) | protein | 260 | 47% helix, 18% strand | A0QC84 |
| B | Carnitinyl-CoA dehydratase (EC 4.2.1.-) | protein | 256 | 43% helix, 18% strand | A0QC84 |
| C | Carnitinyl-CoA dehydratase (EC 4.2.1.-) | protein | 256 | 45% helix, 20% strand | A0QC84 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · 2 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.81 | 0.83 | 122 | EDO |
| 2 | 527 | 0.68 | 0.78 | 51 | BEZ |
| 3 | 437 | 0.64 | 0.77 | 46 | BEZ |
| 4 | 293 | 0.54 | 0.75 | 33 | empty |
| 5 | 72 | 0.34 | 0.76 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1470 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1410 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1398 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3R9S · Structure of a carnitinyl-CoA dehydratase from Mycobacterium avium 104 · 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 A0QC84
- Elsewhere: RCSB PDB 3R9S · PDBe 3R9S · UniProt A0QC84
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