MolNFT v1 · #113343 · protein
Structure of activated aconitase. formation of the (4FE-4S) cluster in the crystal
5ACN: “Structure of activated aconitase. formation of the (4FE-4S) cluster in the crystal”. X-ray diffraction, 3 ligands (F3S, TRC, SO4), 9 pockets (best druggability 0.82). MolNFT v1 #113343 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5ACN
- Type
- protein
- Length
- 754 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aconitase
- EC
- 4.2.1.3
- UniProt
- P16276
- Ligands
- F3S, TRC, SO4
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aconitase (EC 4.2.1.3) | protein | 754 | 34% helix, 20% strand | P16276 |
Ligands and binding sites
- F3S · FE3-S4 cluster · ligand · chains A
- TRC · Tricarballylic acid · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.82 | 0.96 | 49 | SO4, F3S |
| 2 | 278 | 0.64 | 0.81 | 47 | TRC |
| 3 | 265 | 0.54 | 0.76 | 41 | empty |
| 4 | 166 | 0.51 | 0.78 | 28 | empty |
| 5 | 118 | 0.43 | 0.77 | 23 | empty |
Modifications
Observed in the structure: 1 modified (cyclization).
Compared structures
- 5ACN · Structure of activated aconitase. formation of the (4FE-4S) cluster in the crystal · the same entry in another collection · chain A against A, TM-score 1.00
- P16276 · AlphaFold monomer V2.0 prediction for aconitate hydratase, mitochondrial (P16276) · 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 P16276
- Elsewhere: RCSB PDB 5ACN · PDBe 5ACN · UniProt P16276
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