MolNFT v1 · #103837 · protein
Crystal structure of pfuthermo-dbp-RP1 (crystal form II)
4PSM · Ssdna binding protein: “Crystal structure of pfuthermo-dbp-RP1 (crystal form II)”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.77). MolNFT v1 #103837 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4PSM
- Type
- protein
- Length
- 586 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ssdna binding protein
- UniProt
- Q8U208
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ssdna binding protein | protein | 147 | 62% helix, 19% strand | Q8U208 |
| B, C | Ssdna binding protein | protein | 146 | 62% helix, 18% strand | Q8U208 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.77 | 0.85 | 53 | empty |
| 2 | 421 | 0.75 | 0.85 | 56 | empty |
| 3 | 138 | 0.43 | 0.76 | 17 | empty |
| 4 | 60 | 0.30 | 0.75 | 15 | empty |
| 5 | 53 | 0.29 | 0.76 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2002 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1996 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 917 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 897 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 779 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4PSM · Crystal structure of pfuThermo-DBP-RP1 (crystal form II) · 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 4PSM · PDBe 4PSM · UniProt Q8U208
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