MolNFT v1 · #170142 · protein
Crystal structure of haemophilus influenzae 3-isopropylmalate dehydrogenase in complex with O-isobutenyl oxalylhydroxamate.
6XXY: “Crystal structure of haemophilus influenzae 3-isopropylmalate dehydrogenase in complex with O-isobutenyl…”. X-ray diffraction, 3 ligands (NAD, O45, MG), 5 pockets (best druggability 0.77). MolNFT v1 #170142 on GenesisL1: 3D…
- PDB
- 6XXY
- Type
- protein
- Length
- 716 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
- P43860
- Ligands
- NAD, O45, MG
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-isopropylmalate dehydrogenase (EC 1.1.1.85) | protein | 358 | 46% helix, 20% strand | P43860 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- O45 · 2-(2-methylprop-2-enoxyamino)-2-oxidanylidene-ethanoic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 723 | 0.77 | 0.82 | 79 | NAD, O45 |
| 2 | 681 | 0.77 | 0.82 | 75 | NAD, O45 |
| 3 | 301 | 0.61 | 0.79 | 39 | empty |
| 4 | 283 | 0.60 | 0.78 | 29 | empty |
| 5 | 52 | 0.26 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 2701 Ų buried · 53 hydrogen bonds · protein-protein
Compared structures
- 6XXY · Crystal structure of Haemophilus influenzae 3-isopropylmalate dehydrogenase in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P43860 · AlphaFold monomer V2.0 prediction for 3-isopropylmalate dehydrogenase (P43860) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P43860
- Elsewhere: RCSB PDB 6XXY · PDBe 6XXY · UniProt P43860
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