Research workbench
Crystal structure of a putative cytosolic malate dehydrogenase from leishmania major friedlin in complex with NAD
Analyse Crystal structure of a putative cytosolic malate dehydrogenase from leishmania… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I1I
- Type
- protein
- Length
- 633 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- Q4Q7X6
- Ligands
- NAD, PO4
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malate dehydrogenase (EC 1.1.1.37) | protein | 320 | 44% helix, 19% strand | Q4Q7X6 |
| B | Malate dehydrogenase (EC 1.1.1.37) | protein | 313 | 44% helix, 20% strand | Q4Q7X6 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.70 | 0.79 | 51 | NAD, EDO |
| 2 | 633 | 0.67 | 0.76 | 62 | PO4 |
| 3 | 141 | 0.60 | 0.84 | 32 | empty |
| 4 | 344 | 0.55 | 0.75 | 46 | PO4 |
| 5 | 119 | 0.51 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1764 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 4I1I · Crystal structure of a putative Cytosolic malate dehydrogenase from Leishmania major… · 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
- Every structure of UniProt Q4Q7X6
- Elsewhere: RCSB PDB 4I1I · PDBe 4I1I · UniProt Q4Q7X6
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