MolNFT v1 · #93784 · protein
Structure of icdh-1 from M.TUBERCULOSIS complexed with NADPH & MN2+
4HCX · Isocitrate dehydrogenase [NADP]: “Structure of icdh-1 from M.TUBERCULOSIS complexed with NADPH & MN2+”. X-ray diffraction, 3 ligands (NDP, MN, CL), 8 pockets (best druggability 0.60). MolNFT v1 #93784 on GenesisL1: 3D structure…
- PDB
- 4HCX
- Type
- protein
- Length
- 804 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase [NADP]
- EC
- 1.1.1.42
- UniProt
- P65097
- Ligands
- NDP, MN, CL
- Pockets
- 8 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 402 | 47% helix, 22% strand | P65097 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.60 | 0.76 | 52 | NDP, CL |
| 2 | 299 | 0.55 | 0.76 | 33 | empty |
| 3 | 216 | 0.53 | 0.77 | 21 | empty |
| 4 | 147 | 0.47 | 0.77 | 18 | empty |
| 5 | 104 | 0.41 | 0.77 | 22 | CL |
Interfaces
1 interface between chains.
- A–B · 3274 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 4HCX · Structure of ICDH-1 from M.tuberculosis complexed with NADPH & Mn2+ · 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 P65097
- Elsewhere: RCSB PDB 4HCX · PDBe 4HCX · UniProt P65097
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