Research workbench
CU(II) loaded tegillarca granosa ferritin
Analyse CU(II) loaded tegillarca granosa ferritin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KZY
- Type
- protein
- Length
- 673 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin
- EC
- 1.16.3.1
- UniProt
- D3JCC5
- Ligands
- NA, CU
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ferritin (EC 1.16.3.1) | protein | 169 | 74% helix, 0% strand | D3JCC5 |
| B, C, D | Ferritin (EC 1.16.3.1) | protein | 168 | 74% helix, 0% strand | D3JCC5 |
Ligands and binding sites
- NA · Sodium ion · metal · 37 copies · chains A, D, B, C
- CU · Copper (II) ion · metal · 8 copies · chains A, B, D, C
- IPA · Isopropyl alcohol · additive · 4 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.75 | 0.99 | 14 | IPA |
| 2 | 172 | 0.53 | 0.79 | 33 | CU, NA |
| 3 | 191 | 0.49 | 0.76 | 38 | TRS |
| 4 | 55 | 0.43 | 0.83 | 15 | empty |
| 5 | 113 | 0.38 | 0.74 | 21 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1608 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 717 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 710 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 705 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 572 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6KZY · Cu(II) loaded Tegillarca granosa ferritin · 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
- Every structure of UniProt D3JCC5
- Elsewhere: RCSB PDB 6KZY · PDBe 6KZY · UniProt D3JCC5
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