Research workbench
Crystal structure of plant ferritin reveals a novel metal binding site that functions as a transit site for metal transfer in ferritin
Analyse Crystal structure of plant ferritin reveals a novel metal binding site that… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A68
- Type
- protein
- Length
- 4,654 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin-4, chloroplastic
- EC
- 1.16.3.1
- UniProt
- Q948P5
- Ligands
- CA
- Pockets
- 20 · best druggability 0.60
Structure
x-ray diffraction · 5 distinct chains · 70% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, F, G, I, J, K, M, N, O, P, Q, S, T, U, V, W, X | Ferritin-4, chloroplastic (EC 1.16.3.1) | protein | 194 | 69% helix, 1% strand | Q948P5 |
| C | Ferritin-4, chloroplastic (EC 1.16.3.1) | protein | 196 | 70% helix, 1% strand | Q948P5 |
| E | Ferritin-4, chloroplastic (EC 1.16.3.1) | protein | 190 | 71% helix, 1% strand | Q948P5 |
| H, L | Ferritin-4, chloroplastic (EC 1.16.3.1) | protein | 193 | 68% helix, 1% strand | Q948P5 |
| R | Ferritin-4, chloroplastic (EC 1.16.3.1) | protein | 196 | 71% helix, 1% strand | Q948P5 |
Ligands and binding sites
- CA · Calcium ion · metal · 136 copies · chains A, G, H, X, B, C, R, S, D, I, W, E, V, F, J, N, Q, K, P, U, L, M, T, O
- ACY · Acetic acid · additive · 18 copies · chains A, E, F, G, H, I, J, L, M, O, P, Q, R, S, T, V, W, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.60 | 0.77 | 26 | empty |
| 2 | 353 | 0.60 | 0.77 | 25 | empty |
| 3 | 366 | 0.60 | 0.76 | 25 | empty |
| 4 | 369 | 0.60 | 0.76 | 24 | empty |
| 5 | 357 | 0.59 | 0.76 | 25 | empty |
Interfaces
73 interfaces between chains.
- M–S · 1848 Ų buried · 27 hydrogen bonds · protein-protein
- J–X · 1827 Ų buried · 27 hydrogen bonds · protein-protein
- A–G · 1817 Ų buried · 28 hydrogen bonds · protein-protein
- Q–U · 1809 Ų buried · 27 hydrogen bonds · protein-protein
- D–H · 1794 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 3A68 · Crystal structure of plant ferritin reveals a novel metal binding site that functions as… · the same entry in another collection · chain K against K, 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 Q948P5
- Elsewhere: RCSB PDB 3A68 · PDBe 3A68 · UniProt Q948P5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.