MolNFT v1 · #154267 · protein
The crystal structure of isocitrate dehydrogenase KINASE/PHOSPHATASE wtih two MN2+ from E. COLI
6K5L: “The crystal structure of isocitrate dehydrogenase KINASE/PHOSPHATASE wtih two MN2+ from E. COLI”. X-ray diffraction, 3 ligands (AMP, ADP, MN), 20 pockets (best druggability 0.82). MolNFT v1 #154267 on GenesisL1: 3D structure…
- PDB
- 6K5L
- Type
- protein
- Length
- 1,120 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase KINASE/PHOSPHATASE
- EC
- 3.1.3.-
- UniProt
- A0A1Z3UWE5
- Ligands
- AMP, ADP, MN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase KINASE/PHOSPHATASE (EC 3.1.3.-) | protein | 565 | 47% helix, 17% strand | A0A1Z3UWE5 |
| B | Isocitrate dehydrogenase KINASE/PHOSPHATASE (EC 3.1.3.-) | protein | 555 | 47% helix, 17% strand | A0A1Z3UWE5 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.82 | 0.84 | 82 | AMP |
| 2 | 630 | 0.82 | 0.86 | 93 | empty |
| 3 | 135 | 0.78 | 0.96 | 29 | empty |
| 4 | 128 | 0.77 | 0.96 | 27 | empty |
| 5 | 359 | 0.75 | 0.86 | 59 | ADP, MN |
Interfaces
1 interface between chains.
- A–B · 1099 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6K5L · The crystal structure of isocitrate dehydrogenase kinase/phosphatase wtih two Mn2+ from… · 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
- Every structure of UniProt A0A1Z3UWE5
- Elsewhere: RCSB PDB 6K5L · PDBe 6K5L · UniProt A0A1Z3UWE5
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