Research workbench
Directing noble metal ion chemistry within a designed ferritin protein. mercury ions on the three-fold channel
Analyse Directing noble metal ion chemistry within a designed ferritin protein. mercury… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ERZ
- Type
- protein
- Length
- 2,064 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin heavy chain
- EC
- 1.16.3.1
- UniProt
- P02794
- Ligands
- HG, ZN, CA
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Ferritin heavy chain (EC 1.16.3.1) | protein | 172 | 72% helix, 1% strand | P02794 |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- ZN · Zinc ion · metal · 5 copies · chains A, D, B, G, J, H, I
- CA · Calcium ion · metal · 3 copies · chains A, C, E, G, I, K, H, J, L
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 11 copies · chains A, F, B, C, E, G, L, H, I, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.86 | 0.87 | 112 | HG |
| 2 | 102 | 0.80 | 0.99 | 19 | MPD |
| 3 | 105 | 0.79 | 0.98 | 17 | MPD |
| 4 | 417 | 0.71 | 0.82 | 54 | HG |
| 5 | 333 | 0.67 | 0.81 | 40 | HG |
Interfaces
21 interfaces between chains.
- A–F · 1541 Ų buried · 36 hydrogen bonds · protein-protein
- G–L · 1537 Ų buried · 37 hydrogen bonds · protein-protein
- A–E · 732 Ų buried · 13 hydrogen bonds · protein-protein
- G–K · 732 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 727 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3ERZ · Directing Noble Metal Ion Chemistry within a Designed Ferritin Protein. Mercury Ions on… · the same entry in another collection · chain L against L, 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 P02794
- Elsewhere: RCSB PDB 3ERZ · PDBe 3ERZ · UniProt P02794
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