Research workbench
Crystal structure analysis of E173A variant of the soybean ferritin SFER4
Analyse Crystal structure analysis of E173A variant of the soybean ferritin SFER4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A9Q
- Type
- protein
- Length
- 4,629 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 0.59
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F, J, T, W, X | Ferritin-4, chloroplastic (EC 1.16.3.1) | protein | 194 | 71% helix, 1% strand | Q948P5 |
| E | Ferritin-4, chloroplastic (EC 1.16.3.1) | protein | 178 | 71% helix, 1% strand | Q948P5 |
| G, H, I, K, L, M, N, O, P, Q, S, U, V | Ferritin-4, chloroplastic (EC 1.16.3.1) | protein | 193 | 72% helix, 1% strand | Q948P5 |
| R | Ferritin-4, chloroplastic (EC 1.16.3.1) | protein | 196 | 70% helix, 1% strand | Q948P5 |
Ligands and binding sites
- CA · Calcium ion · metal · 124 copies · chains A, G, B, E, F, C, R, S, D, H, V, I, O, W, J, N, Q, K, P, U, L, M, T, X
- 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.59 | 0.76 | 23 | empty |
| 2 | 352 | 0.59 | 0.76 | 25 | empty |
| 3 | 345 | 0.59 | 0.76 | 27 | empty |
| 4 | 345 | 0.59 | 0.76 | 23 | empty |
| 5 | 353 | 0.58 | 0.76 | 26 | empty |
Interfaces
73 interfaces between chains.
- A–G · 1815 Ų buried · 26 hydrogen bonds · protein-protein
- M–S · 1814 Ų buried · 26 hydrogen bonds · protein-protein
- J–X · 1812 Ų buried · 26 hydrogen bonds · protein-protein
- Q–U · 1808 Ų buried · 28 hydrogen bonds · protein-protein
- E–I · 1798 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3A9Q · Crystal Structure Analysis of E173A variant of the soybean ferritin SFER4 · 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 3A9Q · PDBe 3A9Q · UniProt Q948P5
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