MolNFT v1 · #5358 · protein
Structure of human malic enzyme in complex with ketomalonate
1EFK: “Structure of human malic enzyme in complex with ketomalonate”. X-ray diffraction, 3 ligands (NAD, MAK, MG), 20 pockets (best druggability 0.85). MolNFT v1 #5358 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1EFK
- 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, MAK, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Malic enzyme (EC 1.1.1.39) | protein | 553 | 47% helix, 9% strand | P23368 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, D, B, C
- MAK · Alpha-ketomalonic acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium 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 | 954 | 0.85 | 0.86 | 108 | empty |
| 2 | 748 | 0.84 | 0.87 | 89 | empty |
| 3 | 570 | 0.83 | 0.88 | 59 | empty |
| 4 | 582 | 0.82 | 0.87 | 60 | empty |
| 5 | 394 | 0.79 | 0.88 | 60 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2245 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 2242 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 936 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 888 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 828 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 modified (engineered).
Compared structures
- 1EFK · Structure of human malic enzyme in complex with ketomalonate · 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 1EFK · PDBe 1EFK · UniProt P23368
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