Research workbench
Iron-oxo clusters biomineralizing on protein surfaces. structural analysis of H.SALINARUM dpsa in its low and high iron states
Analyse Iron-oxo clusters biomineralizing on protein surfaces. structural analysis of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TKO
- Type
- protein
- Length
- 705 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iron-rich dpsa-homolog protein
- UniProt
- Q9HMP7
- Ligands
- FE, NA, SO4
- Pockets
- 8 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iron-rich dpsa-homolog protein | protein | 180 | 66% helix, 2% strand | Q9HMP7 |
| B, C, D | Iron-rich dpsa-homolog protein | protein | 175 | 68% helix, 2% strand | Q9HMP7 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 38 copies · chains A, C, D, B
- NA · Sodium ion · metal · 2 copies · chains C, A, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.61 | 0.79 | 53 | FE |
| 2 | 299 | 0.60 | 0.79 | 48 | FE |
| 3 | 80 | 0.58 | 0.88 | 24 | empty |
| 4 | 81 | 0.50 | 0.84 | 23 | FE |
| 5 | 81 | 0.46 | 0.82 | 23 | FE |
Interfaces
4 interfaces between chains.
- A–B · 1896 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 1892 Ų buried · 41 hydrogen bonds · protein-protein
- A–D · 1001 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 892 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 1TKO · Iron-oxo clusters biomineralizing on protein surfaces. Structural analysis of H.salinarum… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9HMP7 · AlphaFold monomer V2.0 prediction for DNA protection during starvation protein (Q9HMP7) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q9HMP7
- Elsewhere: RCSB PDB 1TKO · PDBe 1TKO · UniProt Q9HMP7
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