Research workbench
Mature and translocatable forms of glyoxysomal malate dehydrogenase have different activities and stabilities but similar crystal structures
Analyse Mature and translocatable forms of glyoxysomal malate dehydrogenase have… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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