MolNFT v1 · #16500 · protein
Crystal structure of ascaris suum malic enzyme complexed with NADH
1O0S · NAD-dependent malic enzyme: “Crystal structure of ascaris suum malic enzyme complexed with NADH”. X-ray diffraction, 2 ligands (TTN, NAI), 9 pockets (best druggability 0.85). MolNFT v1 #16500 on GenesisL1: 3D structure, binding…
- PDB
- 1O0S
- Type
- protein
- Length
- 1,194 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent malic enzyme
- EC
- 1.1.1.38
- UniProt
- P27443
- Ligands
- TTN, NAI
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent malic enzyme (EC 1.1.1.38) | protein | 602 | 47% helix, 10% strand | P27443 |
| B | NAD-dependent malic enzyme (EC 1.1.1.38) | protein | 592 | 46% helix, 10% strand | P27443 |
Ligands and binding sites
- TTN · Tartronate · ligand · 2 copies · chains A, B
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.85 | 0.85 | 87 | TTN |
| 2 | 689 | 0.76 | 0.81 | 65 | empty |
| 3 | 661 | 0.75 | 0.81 | 61 | empty |
| 4 | 548 | 0.74 | 0.82 | 66 | NAI |
| 5 | 579 | 0.74 | 0.81 | 70 | NAI |
Interfaces
1 interface between chains.
- A–B · 2000 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1O0S · Crystal Structure of Ascaris suum Malic Enzyme Complexed with NADH · the same entry in another collection · chain A against A, TM-score 1.00
- P27443 · AlphaFold monomer V2.0 prediction for NAD-dependent malic enzyme, mitochondrial (P27443) · a predicted model of the same protein · 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 P27443
- Elsewhere: RCSB PDB 1O0S · PDBe 1O0S · UniProt P27443
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