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Anomalous substructure of 3-isopropylmalate dehydrogenase
Analyse Anomalous substructure of 3-isopropylmalate dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2G4O
- Type
- protein
- Length
- 1,348 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-isopropylmalate dehydrogenase
- EC
- 1.1.1.85
- UniProt
- P95313
- Ligands
- CL, SO4
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 3-isopropylmalate dehydrogenase (EC 1.1.1.85) | protein | 337 | 45% helix, 21% strand | P95313 |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.74 | 0.98 | 22 | empty |
| 2 | 62 | 0.73 | 0.98 | 19 | empty |
| 3 | 473 | 0.72 | 0.82 | 39 | empty |
| 4 | 475 | 0.71 | 0.81 | 44 | CL |
| 5 | 469 | 0.69 | 0.80 | 48 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2179 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2137 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 516 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 46 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 26 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2G4O · anomalous substructure of 3-ISOPROPYLMALATE DEHYDROGENASE · 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 P95313
- Elsewhere: RCSB PDB 2G4O · PDBe 2G4O · UniProt P95313
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