MolNFT v1 · #33462 · protein
The structure of the dps-like protein from sulfolobus solfataricus reveals a bacterioferritin-like di-metal binding site within a dps-like dodecameric assembly
2CLB: “The structure of the dps-like protein from sulfolobus solfataricus reveals a bacterioferritin-like di-metal…”. X-ray diffraction, 2 ligands (ZN, FE), 3 pockets (best druggability 0.66). MolNFT v1 #33462 on GenesisL1: 3D structure…
- PDB
- 2CLB
- Type
- protein
- Length
- 1,347 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dps-like protein
- UniProt
- P95855
- Ligands
- ZN, FE
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, M, O | Dps-like protein | protein | 169 | 73% helix, 0% strand | P95855 |
| B | Dps-like protein | protein | 167 | 73% helix, 0% strand | P95855 |
| D, N, P | Dps-like protein | protein | 168 | 74% helix, 0% strand | P95855 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, M, N, O, P
- FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D, M, N, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.66 | 0.81 | 46 | empty |
| 2 | 341 | 0.66 | 0.80 | 47 | empty |
| 3 | 62 | 0.30 | 0.75 | 16 | empty |
Interfaces
10 interfaces between chains.
- M–N · 1359 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1345 Ų buried · 23 hydrogen bonds · protein-protein
- M–O · 993 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 990 Ų buried · 15 hydrogen bonds · protein-protein
- N–O · 547 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 2CLB · The structure of the DPS-like protein from Sulfolobus solfataricus reveals a… · the same entry in another collection · chain P against P, TM-score 1.00
- P95855 · AlphaFold monomer V2.0 prediction for DNA protection during starvation protein (P95855) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P95855
- Elsewhere: RCSB PDB 2CLB · PDBe 2CLB · UniProt P95855
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.