MolNFT v1 · #103615 · protein
Crystal structure of ancestral apicomplexan malate dehydrogenase with malate.
4PLY: “Crystal structure of ancestral apicomplexan malate dehydrogenase with malate.”. X-ray diffraction, 2 ligands (NAI, PYR), 20 pockets (best druggability 0.82). MolNFT v1 #103615 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4PLY
- Type
- protein
- Length
- 2,484 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- Ligands
- NAI, PYR
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, F, E | Malate dehydrogenase | protein | 318 | 48% helix, 20% strand | — |
| C, G | Malate dehydrogenase | protein | 303 | 51% helix, 21% strand | — |
| D, H | Malate dehydrogenase | protein | 303 | 50% helix, 21% strand | — |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 8 copies · chains B, A, C, D, F, E, G, H
- PYR · Pyruvic acid · ligand · 6 copies · chains B, A, D, F, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.82 | 0.90 | 62 | empty |
| 2 | 480 | 0.81 | 0.89 | 73 | empty |
| 3 | 355 | 0.81 | 0.91 | 52 | empty |
| 4 | 344 | 0.80 | 0.90 | 62 | empty |
| 5 | 296 | 0.74 | 0.86 | 29 | empty |
Interfaces
14 interfaces between chains.
- E–H · 2081 Ų buried · 17 hydrogen bonds · protein-protein
- F–G · 1995 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1933 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1925 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1324 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4PLY · Crystal structure of ancestral apicomplexan malate dehydrogenase with malate. · 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 4PLY · PDBe 4PLY
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