MolNFT v1 · #31715 · protein
Structure of an orthorhombic crystal form of human cytosolic aconitase (IRP1)
2B3X · Iron-responsive element binding protein 1: “Structure of an orthorhombic crystal form of human cytosolic aconitase (IRP1)”. X-ray diffraction, 2 ligands (SF4, ZN), 12 pockets (best druggability 0.81). MolNFT v1 #31715 on GenesisL1…
- PDB
- 2B3X
- Type
- protein
- Length
- 888 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iron-responsive element binding protein 1
- EC
- 4.2.1.3
- UniProt
- P21399
- Ligands
- SF4, ZN
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iron-responsive element binding protein 1 (EC 4.2.1.3) | protein | 888 | 39% helix, 19% strand | P21399 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.81 | 0.84 | 106 | SF4 |
| 2 | 334 | 0.70 | 0.83 | 41 | empty |
| 3 | 214 | 0.62 | 0.82 | 43 | empty |
| 4 | 234 | 0.55 | 0.77 | 36 | empty |
| 5 | 155 | 0.47 | 0.76 | 20 | empty |
Compared structures
- 2B3X · Structure of an orthorhombic crystal form of human cytosolic aconitase (IRP1) · the same entry in another collection · chain A against A, TM-score 1.00
- P21399 · AlphaFold monomer V2.0 prediction for cytoplasmic aconitate hydratase (P21399) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P21399
- Elsewhere: RCSB PDB 2B3X · PDBe 2B3X · UniProt P21399
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