MolNFT v1 · #108891 · protein
Crystal structure of citrate bound MDH2
4WLE · Malate dehydrogenase, mitochondrial: “Crystal structure of citrate bound MDH2”. X-ray diffraction, 10 pockets (best druggability 0.74). MolNFT v1 #108891 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4WLE
- 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
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 49% 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 | 49% helix, 19% strand | P40926 |
Ligands and binding sites
- CIT · Citric acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.74 | 0.82 | 60 | CIT |
| 2 | 557 | 0.74 | 0.82 | 78 | CIT |
| 3 | 358 | 0.71 | 0.83 | 49 | CIT |
| 4 | 309 | 0.69 | 0.83 | 47 | CIT |
| 5 | 208 | 0.43 | 0.72 | 28 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1582 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1578 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 470 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 455 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
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 4WLE · PDBe 4WLE · UniProt P40926
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