MolNFT v1 · #103836 · protein
Crystal structure of pfuthermo-dbp-RP1 (crystal form I)
4PSL · Ssdna binding protein: “Crystal structure of pfuthermo-dbp-RP1 (crystal form I)”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.69). MolNFT v1 #103836 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PSL
- Type
- protein
- Length
- 590 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ssdna binding protein
- UniProt
- Q8U208
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ssdna binding protein | protein | 147 | 58% helix, 16% strand | Q8U208 |
| B | Ssdna binding protein | protein | 147 | 61% helix, 16% strand | Q8U208 |
| C, D | Ssdna binding protein | protein | 148 | 55% helix, 20% strand | Q8U208 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.69 | 0.82 | 47 | empty |
| 2 | 277 | 0.68 | 0.83 | 41 | empty |
| 3 | 235 | 0.62 | 0.81 | 37 | empty |
| 4 | 202 | 0.56 | 0.79 | 28 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1938 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1908 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 872 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 860 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 747 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4PSL · Crystal structure of pfuThermo-DBP-RP1 (crystal form I) · 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 Q8U208
- Elsewhere: RCSB PDB 4PSL · PDBe 4PSL · UniProt Q8U208
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