Research workbench
Reconstructed ancestral trichomonad malate dehydrogenase in complex with NADH, SO4, and PO4
Analyse Reconstructed ancestral trichomonad malate dehydrogenase in complex with NADH… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UUP
- Type
- protein
- Length
- 666 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- Ligands
- NAI, PO4, SO4
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malate dehydrogenase (EC 1.1.1.37) | protein | 335 | 46% helix, 19% strand | — |
| B | Malate dehydrogenase (EC 1.1.1.37) | protein | 331 | 46% helix, 19% strand | — |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.72 | 0.79 | 55 | NAI, SO4 |
| 2 | 298 | 0.72 | 0.85 | 41 | NAI, PO4 |
| 3 | 228 | 0.70 | 0.86 | 32 | empty |
| 4 | 306 | 0.60 | 0.78 | 29 | empty |
| 5 | 318 | 0.58 | 0.77 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1616 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 4UUP · Reconstructed ancestral trichomonad malate dehydrogenase in complex with NADH, SO4, and… · the same entry in another collection · 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
- Elsewhere: RCSB PDB 4UUP · PDBe 4UUP
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