Research workbench
Crystal structure of a putative isovaleryl-CoA dehydrogenase (psi- nysgrc-012251) from sinorhizobium meliloti 1021
Analyse Crystal structure of a putative isovaleryl-CoA dehydrogenase (psi… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KTO
- Type
- protein
- Length
- 1,500 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
- Q92VK1
- Ligands
- FAD
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isovaleryl-CoA dehydrogenase (EC 1.3.99.10) | protein | 377 | 58% helix, 15% strand | Q92VK1 |
| B | Isovaleryl-CoA dehydrogenase (EC 1.3.99.10) | protein | 375 | 57% helix, 14% strand | Q92VK1 |
| C | Isovaleryl-CoA dehydrogenase (EC 1.3.99.10) | protein | 374 | 58% helix, 15% strand | Q92VK1 |
| D | Isovaleryl-CoA dehydrogenase (EC 1.3.99.10) | protein | 374 | 56% helix, 15% strand | Q92VK1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, C, B, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.83 | 0.87 | 62 | FAD |
| 2 | 843 | 0.80 | 0.83 | 57 | FAD |
| 3 | 804 | 0.78 | 0.81 | 59 | FAD |
| 4 | 849 | 0.75 | 0.79 | 70 | FAD |
| 5 | 429 | 0.68 | 0.80 | 48 | TRS |
Interfaces
6 interfaces between chains.
- A–B · 1897 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1882 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1811 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 1771 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 209 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 61 modified (engineered).
Compared structures
- 4KTO · Crystal Structure Of a Putative Isovaleryl-CoA dehydrogenase (PSI-NYSGRC-012251) from… · 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 Q92VK1
- Elsewhere: RCSB PDB 4KTO · PDBe 4KTO · UniProt Q92VK1
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