MolNFT v1 · #121747 · protein
DPS4 from nostoc punctiforme in complex with zn ions
5I4J · Ferritin, dps family protein: “DPS4 from nostoc punctiforme in complex with zn ions”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.54). MolNFT v1 #121747 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5I4J
- Type
- protein
- Length
- 708 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin, dps family protein
- UniProt
- B2J981
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 69% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ferritin, dps family protein | protein | 177 | 69% helix, 3% strand | B2J981 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 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 | 189 | 0.54 | 0.79 | 22 | ZN |
| 2 | 212 | 0.51 | 0.76 | 26 | empty |
| 3 | 131 | 0.42 | 0.76 | 20 | empty |
| 4 | 77 | 0.36 | 0.76 | 17 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1977 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 1974 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 1075 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 860 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5I4J · Dps4 from Nostoc punctiforme in complex with Zn 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 5I4J · PDBe 5I4J · UniProt B2J981
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