Research workbench
Crystal structure of malate dehydrogenase from corynebacterium glutamicum atcc 13032 in complex with NAD and malate
Analyse Crystal structure of malate dehydrogenase from corynebacterium glutamicum atcc… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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