MolNFT v1 · #4443 · protein
Crystal structure of a closed form of human mitochondrial NAD(P)+- dependent malic enzyme
1DO8: “Crystal structure of a closed form of human mitochondrial NAD(P)+- dependent malic enzyme”. X-ray diffraction, 3 ligands (NAD, OXL, MN), 20 pockets (best druggability 0.84). MolNFT v1 #4443 on GenesisL1: 3D structure, binding sites…
- PDB
- 1DO8
- Type
- protein
- Length
- 2,212 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malic enzyme
- EC
- 1.1.1.39
- UniProt
- P23368
- Ligands
- NAD, OXL, MN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Malic enzyme (EC 1.1.1.39) | protein | 553 | 48% helix, 10% strand | P23368 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, D, B, C
- OXL · Oxalate ion · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.84 | 0.95 | 34 | empty |
| 2 | 516 | 0.83 | 0.89 | 71 | empty |
| 3 | 554 | 0.82 | 0.88 | 54 | empty |
| 4 | 217 | 0.80 | 0.94 | 29 | empty |
| 5 | 199 | 0.80 | 0.94 | 31 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2267 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2265 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 932 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 904 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 855 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 modified (engineered).
Compared structures
- 1DO8 · Crystal structure of a closed form of human mitochondrial NAD(P)+-dependent malic enzyme · the same entry in another collection · chain A against A, TM-score 1.00
- P23368 · AlphaFold monomer V2.0 prediction for NAD-dependent malic enzyme, mitochondrial (P23368) · 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 P23368
- Elsewhere: RCSB PDB 1DO8 · PDBe 1DO8 · UniProt P23368
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