Research workbench
M. xanthus ferritin-like protein encb
Analyse M. xanthus ferritin-like protein encb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S5K
- Type
- protein
- Length
- 648 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Encb
- UniProt
- Q1D6H3
- Ligands
- FE, CA
- Pockets
- 1 · best druggability 0.50
Structure
x-ray diffraction · 5 distinct chains · 86% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, H, J, D | Encb | protein | 64 | 83% helix, 0% strand | Q1D6H3 |
| B | Encb | protein | 65 | 91% helix, 0% strand | Q1D6H3 |
| E | Encb | protein | 65 | 88% helix, 0% strand | Q1D6H3 |
| G | Encb | protein | 62 | 85% helix, 0% strand | Q1D6H3 |
| I, C | Encb | protein | 68 | 85% helix, 0% strand | Q1D6H3 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 16 copies · chains A, B, E, F, G, H, I, J, C, D
- CA · Calcium ion · metal · 9 copies · chains A, B, E, F, G, H, I, J, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.50 | 0.83 | 18 | empty |
Interfaces
10 interfaces between chains.
- E–F · 1391 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1390 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1344 Ų buried · 21 hydrogen bonds · protein-protein
- I–J · 1332 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1320 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7S5K · M. xanthus ferritin-like protein EncB · 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 Q1D6H3
- Elsewhere: RCSB PDB 7S5K · PDBe 7S5K · UniProt Q1D6H3
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