MolNFT v1 · #3792 · protein
Crystal structure of the wild type halophilic malate dehydrogenase in the apo form
1D3A: “Crystal structure of the wild type halophilic malate dehydrogenase in the apo form”. X-ray diffraction, 2 ligands (NA, CL), 8 pockets (best druggability 0.65). MolNFT v1 #3792 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1D3A
- Type
- protein
- Length
- 606 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Halophilic malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- Q07841
- Ligands
- NA, CL
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Halophilic malate dehydrogenase (EC 1.1.1.37) | protein | 303 | 48% helix, 20% strand | Q07841 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.65 | 0.76 | 49 | empty |
| 2 | 472 | 0.65 | 0.77 | 45 | empty |
| 3 | 101 | 0.38 | 0.76 | 10 | empty |
| 4 | 67 | 0.36 | 0.77 | 16 | empty |
| 5 | 88 | 0.35 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2292 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 1D3A · Crystal structure of the wild type halophilic malate dehydrogenase in the apo form · the same entry in another collection · chain A against A, TM-score 1.00
- Q07841 · AlphaFold monomer V2.0 prediction for malate dehydrogenase (Q07841) · 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 Q07841
- Elsewhere: RCSB PDB 1D3A · PDBe 1D3A · UniProt Q07841
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