Research workbench
Crystal structure of 3-hydroxyacyl-CoA dehydrogenase type-2 from mycobacterium avium
Analyse Crystal structure of 3-hydroxyacyl-CoA dehydrogenase type-2 from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PPI
- Type
- protein
- Length
- 1,023 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxyacyl-CoA dehydrogenase type-2
- EC
- 1.1.1.178, 1.1.1.35
- UniProt
- A0QDP7
- Ligands
- MG
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-hydroxyacyl-CoA dehydrogenase type-2 (EC 1.1.1.178, 1.1.1.35) | protein | 258 | 45% helix, 18% strand | A0QDP7 |
| C | 3-hydroxyacyl-CoA dehydrogenase type-2 (EC 1.1.1.178, 1.1.1.35) | protein | 253 | 44% helix, 18% strand | A0QDP7 |
| D | 3-hydroxyacyl-CoA dehydrogenase type-2 (EC 1.1.1.178, 1.1.1.35) | protein | 254 | 45% helix, 18% strand | A0QDP7 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.86 | 0.87 | 70 | empty |
| 2 | 384 | 0.70 | 0.82 | 52 | MG, GOL |
| 3 | 579 | 0.69 | 0.78 | 58 | MG |
| 4 | 464 | 0.65 | 0.78 | 57 | MG, GOL |
| 5 | 379 | 0.64 | 0.78 | 45 | MG, GOL |
Interfaces
6 interfaces between chains.
- B–D · 1859 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1843 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1542 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1536 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 161 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3PPI · Crystal structure of 3-hydroxyacyl-CoA dehydrogenase type-2 from Mycobacterium avium · 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 A0QDP7
- Elsewhere: RCSB PDB 3PPI · PDBe 3PPI · UniProt A0QDP7
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