Research workbench
2.9 a resolution structure of malate dehydrogenase from archaeoglobus fulgidus in complex with NADH
Analyse 2.9 a resolution structure of malate dehydrogenase from archaeoglobus fulgidus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X0I
- Type
- protein
- Length
- 294 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- O08349
- Ligands
- NAI, NA, SO4
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malate dehydrogenase (EC 1.1.1.37) | protein | 294 | 47% helix, 22% strand | O08349 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · chains A
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.73 | 0.79 | 62 | NAI, SO4 |
| 2 | 52 | 0.30 | 0.76 | 13 | empty |
Compared structures
- 2X0I · 2.9 a resolution structure of malate dehydrogenase from archaeoglobus fulgidus in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- O08349 · AlphaFold monomer V2.0 prediction for malate dehydrogenase (O08349) · 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 O08349
- Elsewhere: RCSB PDB 2X0I · PDBe 2X0I · UniProt O08349
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