MolNFT v1 · #103838 · protein
Crystal structure of apethermo-dbp-RP2
4PSN · Ssdna binding protein: “Crystal structure of apethermo-dbp-RP2”. X-ray diffraction, 20 pockets (best druggability 0.78). MolNFT v1 #103838 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PSN
- Type
- protein
- Length
- 881 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ssdna binding protein
- UniProt
- Q9YAS7
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ssdna binding protein | protein | 220 | 41% helix, 34% strand | Q9YAS7 |
| B | Ssdna binding protein | protein | 219 | 42% helix, 34% strand | Q9YAS7 |
| C, D | Ssdna binding protein | protein | 221 | 38% helix, 33% strand | Q9YAS7 |
Ligands and binding sites
- IMD · Imidazole · additive · 6 copies · chains A, D, B, C
- GOL · Glycerol · additive · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.78 | 0.89 | 36 | empty |
| 2 | 352 | 0.78 | 0.88 | 40 | GOL, IMD |
| 3 | 511 | 0.66 | 0.77 | 75 | IMD |
| 4 | 347 | 0.58 | 0.77 | 36 | IMD |
| 5 | 332 | 0.57 | 0.76 | 38 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2837 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 2801 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 903 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 900 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 886 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 4PSN · Crystal structure of apeThermo-DBP-RP2 · 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 Q9YAS7
- Elsewhere: RCSB PDB 4PSN · PDBe 4PSN · UniProt Q9YAS7
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