Research workbench
Crystal structure of malate dehydrogenase from burkholderia pseudomallei
Analyse Crystal structure of malate dehydrogenase from burkholderia pseudomallei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D5T
- Type
- protein
- Length
- 1,286 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- Q3JKE9
- Ligands
- NA, MG
- Pockets
- 18 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Malate dehydrogenase (EC 1.1.1.37) | protein | 321 | 46% helix, 17% strand | Q3JKE9 |
| C | Malate dehydrogenase (EC 1.1.1.37) | protein | 323 | 44% helix, 19% strand | Q3JKE9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 478 | 0.64 | 0.77 | 53 | empty |
| 2 | 402 | 0.62 | 0.77 | 38 | empty |
| 3 | 413 | 0.60 | 0.76 | 51 | empty |
| 4 | 407 | 0.60 | 0.76 | 50 | empty |
| 5 | 337 | 0.59 | 0.77 | 34 | MG |
Interfaces
3 interfaces between chains.
- A–B · 1473 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1455 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 137 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3D5T · Crystal structure of malate dehydrogenase from Burkholderia pseudomallei · the same entry in another collection · chain A against A, TM-score 1.00
- Q3JKE9 · AlphaFold monomer V2.0 prediction for malate dehydrogenase (Q3JKE9) · 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 Q3JKE9
- Elsewhere: RCSB PDB 3D5T · PDBe 3D5T · UniProt Q3JKE9
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