Research workbench
Crystal structure of ancestral apicomplexan malate dehydrogenase with oxamate.
Analyse Crystal structure of ancestral apicomplexan malate dehydrogenase with oxamate. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PLH
- Type
- protein
- Length
- 1,247 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- Ligands
- OXM, NAI, NA
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malate dehydrogenase | protein | 313 | 52% helix, 20% strand | — |
| B | Malate dehydrogenase | protein | 313 | 50% helix, 20% strand | — |
| C | Malate dehydrogenase | protein | 305 | 52% helix, 21% strand | — |
| D | Malate dehydrogenase | protein | 316 | 50% helix, 20% strand | — |
Ligands and binding sites
- OXM · Oxamic acid · ligand · 4 copies · chains A, B, C, D
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.86 | 0.87 | 128 | empty |
| 2 | 607 | 0.78 | 0.84 | 80 | OXM, NAI |
| 3 | 212 | 0.74 | 0.90 | 29 | empty |
| 4 | 195 | 0.73 | 0.89 | 25 | empty |
| 5 | 557 | 0.68 | 0.78 | 61 | OXM, NA, NAI |
Interfaces
6 interfaces between chains.
- C–D · 2038 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 2000 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1326 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1320 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 595 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4PLH · Crystal structure of ancestral apicomplexan malate dehydrogenase with oxamate. · 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 4PLH · PDBe 4PLH
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