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Crystal structure of cytoplasmic metal binding domain with iron ions
Analyse Crystal structure of cytoplasmic metal binding domain with iron ions in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IU9
- Type
- protein
- Length
- 585 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VIT1
- Ligands
- ZN, FE2
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | VIT1 | protein | 72 | 75% 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 · 20 copies · chains A, D, B, C, E, H, F, I
- FE2 · Fe (II) ion · metal · 7 copies · chains A, B, C, D, E, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.57 | 0.75 | 48 | empty |
| 2 | 263 | 0.53 | 0.75 | 29 | empty |
| 3 | 268 | 0.52 | 0.75 | 32 | empty |
| 4 | 264 | 0.50 | 0.74 | 23 | empty |
| 5 | 81 | 0.34 | 0.75 | 17 | empty |
Interfaces
10 interfaces between chains.
- A–B · 846 Ų buried · 2 hydrogen bonds · protein-protein
- E–F · 833 Ų buried · 2 hydrogen bonds · protein-protein
- H–I · 800 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 731 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 529 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6IU9 · Crystal structure of cytoplasmic metal binding domain with iron 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 6IU9 · PDBe 6IU9
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