MolNFT v1 · #66034 · protein
Crystal structure of staphylococcal nuclease variant DELTA+PHS T62R at cryogenic temperature
3HEJ · Thermonuclease: “Crystal structure of staphylococcal nuclease variant DELTA+PHS T62R at cryogenic temperature”. X-ray diffraction, 1 ligand (THP), 7 pockets (best druggability 0.69). MolNFT v1 #66034 on GenesisL1: 3D structure…
- PDB
- 3HEJ
- Type
- protein
- Length
- 540 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermonuclease
- EC
- 3.1.31.1
- UniProt
- P00644
- Ligands
- THP
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, B, C | Thermonuclease (EC 3.1.31.1) | protein | 135 | 27% helix, 27% strand | P00644 |
Ligands and binding sites
- THP · Thymidine-3',5'-diphosphate · ligand · 4 copies · chains A, D, B, C
- GOL · Glycerol · additive · 2 copies · chains A, B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.69 | 0.78 | 46 | THP, MRD |
| 2 | 429 | 0.61 | 0.76 | 31 | empty |
| 3 | 429 | 0.61 | 0.76 | 29 | empty |
| 4 | 102 | 0.43 | 0.77 | 16 | THP |
| 5 | 64 | 0.40 | 0.80 | 12 | THP |
Interfaces
4 interfaces between chains.
- A–D · 1412 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1400 Ų buried · 19 hydrogen bonds · protein-protein
- D–B · 321 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 39 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3HEJ · Crystal structure of Staphylococcal nuclease variant Delta+PHS T62R at cryogenic… · 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 P00644
- Elsewhere: RCSB PDB 3HEJ · PDBe 3HEJ · UniProt P00644
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