Research workbench
Structural features stabilizing halophilic malate dehydrogenase from an archaebacterium
Analyse Structural features stabilizing halophilic malate dehydrogenase from an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HLP
- Type
- protein
- Length
- 606 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- Q07841
- Ligands
- NAD
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Malate dehydrogenase (EC 1.1.1.37) | protein | 303 | 40% helix, 17% strand | Q07841 |
Ligands and binding sites
- 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.64 | 0.78 | 45 | NAD |
| 2 | 429 | 0.64 | 0.77 | 47 | NAD |
| 3 | 85 | 0.34 | 0.75 | 19 | empty |
| 4 | 57 | 0.33 | 0.77 | 11 | empty |
| 5 | 52 | 0.32 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2090 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 1HLP · Structural features stabilizing halophilic malate dehydrogenase from an archaebacterium · 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 0.98
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 1HLP · PDBe 1HLP · UniProt Q07841
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