Research workbench
Crystal structure of ancestral apicomplexan malate dehydrogenase with lactate.
Analyse Crystal structure of ancestral apicomplexan malate dehydrogenase with lactate. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PLW
- Type
- protein
- Length
- 1,261 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- Ligands
- NAI, PO4
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malate dehydrogenase | protein | 317 | 51% helix, 20% strand | — |
| B | Malate dehydrogenase | protein | 313 | 50% helix, 20% strand | — |
| C | Malate dehydrogenase | protein | 316 | 51% helix, 20% strand | — |
| D | Malate dehydrogenase | protein | 315 | 51% helix, 20% strand | — |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.79 | 0.88 | 56 | empty |
| 2 | 419 | 0.79 | 0.88 | 55 | empty |
| 3 | 472 | 0.78 | 0.86 | 60 | NAI, PO4 |
| 4 | 263 | 0.72 | 0.86 | 32 | empty |
| 5 | 478 | 0.72 | 0.81 | 51 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1996 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1990 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1323 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1274 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 477 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4PLW · Crystal structure of ancestral apicomplexan malate dehydrogenase with lactate. · 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 4PLW · PDBe 4PLW
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