MolNFT v1 · #10569 · protein
Structure of human isovaleryl-CoA dehydrogenase at 2.6 ångströms resolution: structural basis for substrate specificity
1IVH: “Structure of human isovaleryl-CoA dehydrogenase at 2.6 ångströms resolution: structural basis for substrate…”. X-ray diffraction, 2 ligands (FAD, COS), 17 pockets (best druggability 0.84). MolNFT v1 #10569 on GenesisL1: 3D…
- PDB
- 1IVH
- Type
- protein
- Length
- 1,548 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isovaleryl-CoA dehydrogenase
- EC
- 1.3.99.10
- UniProt
- P26440
- Ligands
- FAD, COS
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Isovaleryl-CoA dehydrogenase (EC 1.3.99.10) | protein | 387 | 57% helix, 15% strand | P26440 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, D, C
- COS · Coenzyme A persulfide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.84 | 0.88 | 64 | FAD, COS |
| 2 | 654 | 0.84 | 0.88 | 67 | FAD, COS |
| 3 | 634 | 0.84 | 0.88 | 63 | FAD, COS |
| 4 | 656 | 0.83 | 0.87 | 72 | FAD, COS |
| 5 | 406 | 0.71 | 0.83 | 44 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1971 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1930 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 1697 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1691 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 204 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1IVH · Structure of human isovaleryl-CoA dehydrogenase at 2.6 ångströms resolution: structural… · the same entry in another collection · chain A against A, TM-score 1.00
- P26440 · AlphaFold monomer V2.0 prediction for isovaleryl-CoA dehydrogenase, mitochondrial (P26440) · a predicted model of the same protein · 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 P26440
- Elsewhere: RCSB PDB 1IVH · PDBe 1IVH · UniProt P26440
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