MolNFT v1 · #108900 · protein
Crystal structure of oxaloacetate and NADH bound MDH2
4WLO · Malate dehydrogenase, mitochondrial: “Crystal structure of oxaloacetate and NADH bound MDH2”. X-ray diffraction, 2 ligands (NAI, OAA), 12 pockets (best druggability 0.73). MolNFT v1 #108900 on GenesisL1: 3D structure, binding sites…
- PDB
- 4WLO
- Type
- protein
- Length
- 1,256 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase, mitochondrial
- EC
- 1.1.1.37
- UniProt
- P40926
- Ligands
- NAI, OAA
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Malate dehydrogenase, mitochondrial (EC 1.1.1.37) | protein | 314 | 48% helix, 19% strand | P40926 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- OAA · Oxaloacetate ion · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.73 | 0.86 | 47 | NAI, OAA |
| 2 | 293 | 0.73 | 0.86 | 42 | NAI, OAA |
| 3 | 253 | 0.72 | 0.87 | 42 | NAI, OAA |
| 4 | 228 | 0.72 | 0.87 | 39 | NAI, OAA |
| 5 | 243 | 0.48 | 0.73 | 48 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1599 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1575 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 424 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 417 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4WLO · Crystal structure of oxaloacetate and NADH bound MDH2 · the same entry in another collection · chain A against A, TM-score 1.00
- P40926 · AlphaFold monomer V2.0 prediction for malate dehydrogenase, mitochondrial (P40926) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P40926
- Elsewhere: RCSB PDB 4WLO · PDBe 4WLO · UniProt P40926
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