MolNFT v1 · #124613 · protein
E. COLI malate dehydrogenase with the inhibitor 6DHNAD
5KKA: “E. COLI malate dehydrogenase with the inhibitor 6DHNAD”. X-ray diffraction, 1 ligand (6V0), 7 pockets (best druggability 0.59). MolNFT v1 #124613 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KKA
- Type
- protein
- Length
- 601 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- P61889
- Ligands
- 6V0
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malate dehydrogenase (EC 1.1.1.37) | protein | 300 | 49% helix, 18% strand | P61889 |
| B | Malate dehydrogenase (EC 1.1.1.37) | protein | 301 | 49% helix, 18% strand | P61889 |
Ligands and binding sites
- 6V0 · [[(2~{R},3~{S},4~{R},5~{R})-5-(5-aminocarbonyl-2~{H}-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.59 | 0.77 | 48 | 6V0 |
| 2 | 282 | 0.54 | 0.76 | 41 | 6V0 |
| 3 | 92 | 0.41 | 0.78 | 17 | empty |
| 4 | 99 | 0.35 | 0.74 | 18 | empty |
| 5 | 97 | 0.35 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1564 Ų buried · 26 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 P61889
- Elsewhere: RCSB PDB 5KKA · PDBe 5KKA · UniProt P61889
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