MolNFT v1 · #103610 · protein
Crystal structure of ancestral apicomplexan malate dehydrogenase with oxamate.
4PLT: “Crystal structure of ancestral apicomplexan malate dehydrogenase with oxamate.”. X-ray diffraction, 2 ligands (NAI, OXM), 16 pockets (best druggability 0.87). MolNFT v1 #103610 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4PLT
- Type
- protein
- Length
- 1,274 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- Ligands
- NAI, OXM
- Pockets
- 16 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Malate dehydrogenase | protein | 319 | 50% helix, 20% strand | — |
| C, D | Malate dehydrogenase | protein | 318 | 50% helix, 20% strand | — |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains B, A, C, D
- OXM · Oxamic acid · ligand · 4 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.87 | 0.88 | 146 | empty |
| 2 | 637 | 0.79 | 0.84 | 96 | NAI, OXM |
| 3 | 675 | 0.79 | 0.83 | 96 | NAI, OXM |
| 4 | 179 | 0.73 | 0.90 | 26 | empty |
| 5 | 185 | 0.73 | 0.90 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2061 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 2000 Ų buried · 15 hydrogen bonds · protein-protein
- B–A · 1327 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1253 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 595 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4PLT · Crystal structure of ancestral apicomplexan malate dehydrogenase with oxamate. · the same entry in another collection · chain B against B, 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 4PLT · PDBe 4PLT
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