Research workbench
Crystal structure of human M-NAD-me in ternary complex with NAD and LU3+
Analyse Crystal structure of human M-NAD-me in ternary complex with NAD and LU3+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PJL
- Type
- protein
- Length
- 4,408 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent malic enzyme, mitochondrial
- EC
- 1.1.1.38
- UniProt
- P23368
- Ligands
- NAD, LU
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | NAD-dependent malic enzyme, mitochondrial (EC 1.1.1.38) | protein | 551 | 48% helix, 9% strand | P23368 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 16 copies · chains A, B, C, D, E, F, G, H
- LU · Lutetium (III) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
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 | 605 | 0.86 | 0.91 | 99 | empty |
| 2 | 643 | 0.86 | 0.90 | 98 | empty |
| 3 | 711 | 0.85 | 0.89 | 121 | empty |
| 4 | 654 | 0.85 | 0.89 | 108 | empty |
| 5 | 619 | 0.83 | 0.87 | 58 | empty |
Interfaces
12 interfaces between chains.
- G–H · 2265 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2252 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 2249 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 2204 Ų buried · 20 hydrogen bonds · protein-protein
- E–G · 718 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 112 modified (engineered).
Compared structures
- 1PJL · Crystal structure of human m-NAD-ME in ternary complex with NAD and Lu3+ · the same entry in another collection · chain H against H, 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 0.98
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 1PJL · PDBe 1PJL · UniProt P23368
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