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Crystal structure of cytoplasmic metal binding domain with zinc ions
Analyse Crystal structure of cytoplasmic metal binding domain with zinc ions in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IU5
- Type
- protein
- Length
- 585 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.25
- Source
- Eucalyptus grandis
- Molecule
- VIT1
- Ligands
- ZN, CL
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · resolution 2.25 · 3 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | VIT1 | protein | 72 | 76% helix, 0% strand | — |
| B, E, F | VIT1 | protein | 74 | 72% helix, 0% strand | — |
| C, H, I | VIT1 | protein | 73 | 73% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 27 copies · chains A, D, B, C, E, H, F, I
- CL · Chloride ion · ion · 6 copies · chains A, B, C, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 647 | 0.66 | 0.75 | 57 | empty |
| 2 | 290 | 0.56 | 0.76 | 29 | empty |
| 3 | 278 | 0.50 | 0.74 | 28 | empty |
| 4 | 92 | 0.36 | 0.75 | 16 | empty |
Interfaces
10 interfaces between chains.
- A–B · 853 Ų buried · 2 hydrogen bonds · protein-protein
- E–F · 853 Ų buried · 2 hydrogen bonds · protein-protein
- H–I · 837 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 764 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 523 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6IU5 · Crystal structure of cytoplasmic metal binding domain with zinc ions · 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
- Elsewhere: RCSB PDB 6IU5 · PDBe 6IU5
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