Research workbench
DPS4 from nostoc punctiforme in complex with fe ions
Analyse DPS4 from nostoc punctiforme in complex with fe ions in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HJH
- Type
- protein
- Length
- 709 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin, dps family protein
- UniProt
- B2J981
- Ligands
- FE
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ferritin, dps family protein | protein | 177 | 70% helix, 3% strand | B2J981 |
| D | Ferritin, dps family protein | protein | 178 | 70% helix, 3% strand | B2J981 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.53 | 0.78 | 25 | FE |
| 2 | 196 | 0.50 | 0.77 | 25 | empty |
| 3 | 133 | 0.44 | 0.76 | 19 | empty |
| 4 | 59 | 0.30 | 0.75 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2005 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 1997 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 1109 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 837 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5HJH · Dps4 from Nostoc punctiforme in complex with Fe ions · 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 B2J981
- Elsewhere: RCSB PDB 5HJH · PDBe 5HJH · UniProt B2J981
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