MolNFT v1 · #88113 · protein
1.70 a resolution structure of the malate dehydrogenase from chloroflexus aurantiacus
4CL3: “1.70 a resolution structure of the malate dehydrogenase from chloroflexus aurantiacus”. X-ray diffraction, 2 ligands (CD, CL), 3 pockets (best druggability 0.71). MolNFT v1 #88113 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4CL3
- Type
- protein
- Length
- 618 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- B9LLP6
- Ligands
- CD, CL
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Malate dehydrogenase (EC 1.1.1.37) | protein | 309 | 51% helix, 21% strand | B9LLP6 |
Ligands and binding sites
- CD · Cadmium ion · metal · 11 copies · chains A, D
- CL · Chloride ion · ion · chains A
- ACT · Acetate ion · additive · 5 copies · chains A, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.71 | 0.79 | 52 | CD, ACT, PEG |
| 2 | 493 | 0.63 | 0.76 | 51 | PEG |
| 3 | 428 | 0.63 | 0.77 | 62 | ACT |
Interfaces
1 interface between chains.
- A–D · 1142 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 4CL3 · 1.70 A resolution structure of the malate dehydrogenase from Chloroflexus aurantiacus · the same entry in another collection · chain A against A, TM-score 1.00
- B9LLP6 · AlphaFold monomer V2.0 prediction for malate dehydrogenase (B9LLP6) · 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 B9LLP6
- Elsewhere: RCSB PDB 4CL3 · PDBe 4CL3 · UniProt B9LLP6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.