MolNFT v1 · #41327 · protein
Crystal structure of human IBA2, orthorhombic crystal form
2JJZ · Ionized calcium-binding adapter molecule 2: “Crystal structure of human IBA2, orthorhombic crystal form”. X-ray diffraction, 3 ligands (ZN, NA, CL), 3 pockets (best druggability 0.68). MolNFT v1 #41327 on GenesisL1: 3D structure…
- PDB
- 2JJZ
- Type
- protein
- Length
- 418 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ionized calcium-binding adapter molecule 2
- UniProt
- Q9BQI0
- Ligands
- ZN, NA, CL
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 62% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ionized calcium-binding adapter molecule 2 | protein | 110 | 64% helix, 2% strand | Q9BQI0 |
| B | Ionized calcium-binding adapter molecule 2 | protein | 112 | 66% helix, 2% strand | Q9BQI0 |
| C | Ionized calcium-binding adapter molecule 2 | protein | 115 | 63% helix, 2% strand | Q9BQI0 |
| D | Ionized calcium-binding adapter molecule 2 | protein | 81 | 52% helix, 2% strand | Q9BQI0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains C
- CL · Chloride ion · ion · 2 copies · chains B, C
- ACT · Acetate ion · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 572 | 0.68 | 0.77 | 63 | empty |
| 2 | 278 | 0.60 | 0.79 | 41 | ACT |
| 3 | 191 | 0.56 | 0.80 | 26 | empty |
Interfaces
3 interfaces between chains.
- B–C · 794 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 445 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 412 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2JJZ · Crystal Structure of Human Iba2, orthorhombic crystal form · the same entry in another collection · chain D against D, TM-score 1.00
- Q9BQI0 · AlphaFold monomer V2.0 prediction for allograft inflammatory factor 1-like (Q9BQI0) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9BQI0
- Elsewhere: RCSB PDB 2JJZ · PDBe 2JJZ · UniProt Q9BQI0
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