MolNFT v1 · #21824 · protein
Mature and translocatable forms of glyoxysomal malate dehydrogenase have different activities and stabilities but similar crystal structures
1SMK · Malate dehydrogenase, glyoxysomal: “Mature and translocatable forms of glyoxysomal malate dehydrogenase have different activities and stabilities…”. X-ray diffraction, 20 pockets (best druggability 0.78). MolNFT v1 #21824 on…
- PDB
- 1SMK
- Type
- protein
- Length
- 2,504 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase, glyoxysomal
- EC
- 1.1.1.37
- UniProt
- P19446
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Malate dehydrogenase, glyoxysomal (EC 1.1.1.37) | protein | 313 | 48% helix, 19% strand | P19446 |
Ligands and binding sites
- CIT · Citric acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 800 | 0.78 | 0.82 | 80 | empty |
| 2 | 944 | 0.76 | 0.79 | 108 | empty |
| 3 | 533 | 0.74 | 0.82 | 65 | empty |
| 4 | 587 | 0.72 | 0.80 | 62 | empty |
| 5 | 533 | 0.72 | 0.81 | 58 | empty |
Interfaces
10 interfaces between chains.
- E–F · 1674 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1659 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 1656 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1612 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 765 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1SMK · Mature and translocatable forms of glyoxysomal malate dehydrogenase have different… · the same entry in another collection · chain H against H, TM-score 1.00
- P19446 · AlphaFold monomer V2.0 prediction for malate dehydrogenase, glyoxysomal (P19446) · 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 P19446
- Elsewhere: RCSB PDB 1SMK · PDBe 1SMK · UniProt P19446
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