MolNFT v1 · #110601 · protein
Crystal structure of 3-isopropylmalate dehydrogenase (SACI_0600) from sulfolobus acidocaldarius complex with 3-isopropylmalate and MG2+
4Y1P: “Crystal structure of 3-isopropylmalate dehydrogenase (SACI_0600) from sulfolobus acidocaldarius complex with…”. X-ray diffraction, 3 ligands (IPM, MG, SO4), 5 pockets (best druggability 0.65). MolNFT v1 #110601 on GenesisL1: 3D…
- PDB
- 4Y1P
- Type
- protein
- Length
- 671 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-isopropylmalate dehydrogenase
- EC
- 1.1.1.85
- UniProt
- Q4JB37
- Ligands
- IPM, MG, SO4
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-isopropylmalate dehydrogenase (EC 1.1.1.85) | protein | 335 | 48% helix, 21% strand | Q4JB37 |
| B | 3-isopropylmalate dehydrogenase (EC 1.1.1.85) | protein | 336 | 46% helix, 21% strand | Q4JB37 |
Ligands and binding sites
- IPM · 3-isopropylmalic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.65 | 0.81 | 33 | empty |
| 2 | 353 | 0.59 | 0.76 | 31 | SO4 |
| 3 | 112 | 0.43 | 0.77 | 20 | MG, IPM |
| 4 | 110 | 0.40 | 0.77 | 20 | MG, IPM |
| 5 | 51 | 0.28 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 401 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4Y1P · Crystal structure of 3-isopropylmalate dehydrogenase (Saci_0600) from Sulfolobus… · 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 Q4JB37
- Elsewhere: RCSB PDB 4Y1P · PDBe 4Y1P · UniProt Q4JB37
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