Research workbench
Crystal structure of aconitase with trans-aconitate and nitrocitrate bound
Analyse Crystal structure of aconitase with trans-aconitate and nitrocitrate bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NIS
- Type
- protein
- Length
- 753 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aconitase
- EC
- 4.2.1.3
- UniProt
- P20004
- Ligands
- SF4, NTC
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aconitase (EC 4.2.1.3) | protein | 753 | 35% helix, 21% strand | P20004 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- NTC · 2-hydroxy-2-nitromethyl succinic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.74 | 0.98 | 27 | SF4, NTC |
| 2 | 70 | 0.72 | 0.97 | 23 | empty |
| 3 | 315 | 0.62 | 0.79 | 49 | empty |
| 4 | 251 | 0.54 | 0.77 | 40 | empty |
| 5 | 144 | 0.50 | 0.79 | 27 | empty |
Compared structures
- 1NIS · Crystal structure of aconitase with trans-aconitate and nitrocitrate bound · the same entry in another collection · chain A against A, TM-score 1.00
- P20004 · AlphaFold monomer V2.0 prediction for aconitate hydratase, mitochondrial (P20004) · a predicted model of the same protein · 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 P20004
- Elsewhere: RCSB PDB 1NIS · PDBe 1NIS · UniProt P20004
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