Research workbench
Crystal structure of human mitochondrial NAD(P)+-dependent malic enzyme in a pentary complex with natural substrate malate, cofactor NADH, mn++, and allosteric activator fumarate
Analyse Crystal structure of human mitochondrial NAD(P)+-dependent malic enzyme in a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PJ2
- Type
- protein
- Length
- 2,212 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent malic enzyme, mitochondrial
- EC
- 1.1.1.39
- UniProt
- P23368
- Ligands
- NAI, LMR, FUM, MN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | NAD-dependent malic enzyme, mitochondrial (EC 1.1.1.39) | protein | 553 | 49% helix, 10% strand | P23368 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 8 copies · chains A, D, B, C
- LMR · (2S)-2-hydroxybutanedioic acid · ligand · 4 copies · chains A, B, C, D
- FUM · Fumaric acid · 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 | 1153 | 0.86 | 0.87 | 166 | empty |
| 2 | 244 | 0.83 | 0.95 | 46 | FUM |
| 3 | 194 | 0.83 | 0.96 | 27 | empty |
| 4 | 194 | 0.83 | 0.96 | 30 | empty |
| 5 | 280 | 0.77 | 0.89 | 43 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2330 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2318 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1021 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 987 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 805 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 modified (engineered).
Compared structures
- 1PJ2 · Crystal structure of human mitochondrial NAD(P)+-dependent malic enzyme in a pentary… · 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 1PJ2 · PDBe 1PJ2 · UniProt P23368
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