Research workbench
Structure of dpsl (DNA protection in starved cells - like) from pyrococcus furiosus
Analyse Structure of dpsl (DNA protection in starved cells - like) from pyrococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7STW
- Type
- protein
- Length
- 2,040 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA protection during starvation protein
- EC
- 1.16.-.-
- UniProt
- Q8U1L3
- Ligands
- ZN, FE
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 1 distinct chain · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | DNA protection during starvation protein (EC 1.16.-.-) | protein | 170 | 69% helix, 0% strand | Q8U1L3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- FE · Fe (III) ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1149 | 0.81 | 0.82 | 135 | empty |
| 2 | 911 | 0.79 | 0.81 | 108 | empty |
| 3 | 783 | 0.79 | 0.82 | 99 | empty |
| 4 | 362 | 0.78 | 0.87 | 54 | empty |
| 5 | 307 | 0.77 | 0.88 | 50 | empty |
Interfaces
30 interfaces between chains.
- F–K · 1386 Ų buried · 16 hydrogen bonds · protein-protein
- C–J · 1371 Ų buried · 16 hydrogen bonds · protein-protein
- B–G · 1368 Ų buried · 14 hydrogen bonds · protein-protein
- A–L · 1315 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 1305 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7STW · Structure of DPSL (DNA Protection in Starved Cells - Like) from Pyrococcus furiosus · the same entry in another collection · chain L against L, 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 Q8U1L3
- Elsewhere: RCSB PDB 7STW · PDBe 7STW · UniProt Q8U1L3
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