Research workbench
Crystal structure of isocitrate lyase (Caur_3889) from Chloroflexus aurantiacus in complex with isocitrate and manganese ion
Analyse Crystal structure of isocitrate lyase (Caur_3889) from Chloroflexus aurantiacus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LRT
- Type
- protein
- Length
- 3,384 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)
- Molecule
- Isocitrate lyase
- UniProt
- A9WDE7
- Ligands
- ICT, MN
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · resolution 2.9 · 1 distinct chain · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J, M, P, S, V | Isocitrate lyase | protein | 423 | 50% helix, 12% strand | A9WDE7 |
Ligands and binding sites
- ICT · Isocitric acid · ligand · 8 copies · chains A, D, G, J, M, P, S, V
- MN · Manganese (II) ion · metal · 8 copies · chains A, D, G, J, M, P, S, V
- GOL · Glycerol · additive · 12 copies · chains A, G, D, J, P, V, S, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.88 | 0.96 | 100 | empty |
| 2 | 522 | 0.88 | 0.94 | 73 | GOL |
| 3 | 524 | 0.88 | 0.94 | 74 | empty |
| 4 | 437 | 0.88 | 0.95 | 81 | GOL |
| 5 | 585 | 0.87 | 0.92 | 78 | empty |
Interfaces
19 interfaces between chains.
- S–V · 5072 Ų buried · 76 hydrogen bonds · protein-protein
- G–J · 5059 Ų buried · 84 hydrogen bonds · protein-protein
- A–D · 5008 Ų buried · 76 hydrogen bonds · protein-protein
- M–P · 4998 Ų buried · 78 hydrogen bonds · protein-protein
- D–J · 2000 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6LRT · Crystal structure of isocitrate lyase (CAUR_3889) from chloroflexus aurantiacus in… · 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 A9WDE7
- Elsewhere: RCSB PDB 6LRT · PDBe 6LRT · UniProt A9WDE7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.