MolNFT v1 · #152790 · protein
Crystal structure of malate dehydrogenase from corynebacterium glutamicum atcc 13032 in complex with NAD and malate
6ITK: “Crystal structure of malate dehydrogenase from corynebacterium glutamicum atcc 13032 in complex with NAD and…”. X-ray diffraction, 2 ligands (LMR, NAD), 6 pockets (best druggability 0.65). MolNFT v1 #152790 on GenesisL1: 3D…
- PDB
- 6ITK
- Type
- protein
- Length
- 636 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- Q8NN33
- Ligands
- LMR, NAD
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Malate dehydrogenase (EC 1.1.1.37) | protein | 318 | 47% helix, 18% strand | Q8NN33 |
Ligands and binding sites
- LMR · (2S)-2-hydroxybutanedioic acid · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.65 | 0.78 | 60 | empty |
| 2 | 451 | 0.64 | 0.78 | 50 | LMR, NAD |
| 3 | 425 | 0.62 | 0.77 | 48 | LMR, NAD |
| 4 | 170 | 0.47 | 0.76 | 28 | empty |
| 5 | 81 | 0.46 | 0.82 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1576 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6ITK · Crystal structure of malate dehydrogenase from Corynebacterium glutamicum ATCC 13032 in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NN33 · AlphaFold monomer V2.0 prediction for malate dehydrogenase (Q8NN33) · 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 Q8NN33
- Elsewhere: RCSB PDB 6ITK · PDBe 6ITK · UniProt Q8NN33
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