MolNFT v1 · #65985 · protein
Crystal structure of TM1865, an endonuclease V from thermotoga maritima
3HD0: “Crystal structure of TM1865, an endonuclease V from thermotoga maritima”. X-ray diffraction, 7 pockets (best druggability 0.51). MolNFT v1 #65985 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3HD0
- Type
- protein
- Length
- 659 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease V
- EC
- 3.1.21.7
- UniProt
- Q9X2H9
- Pockets
- 7 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease V (EC 3.1.21.7) | protein | 220 | 25% helix, 26% strand | Q9X2H9 |
| B | Endonuclease V (EC 3.1.21.7) | protein | 216 | 27% helix, 28% strand | Q9X2H9 |
| D | Endonuclease V (EC 3.1.21.7) | protein | 223 | 26% helix, 27% strand | Q9X2H9 |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.51 | 0.79 | 28 | empty |
| 2 | 139 | 0.49 | 0.78 | 29 | empty |
| 3 | 121 | 0.48 | 0.79 | 19 | empty |
| 4 | 222 | 0.48 | 0.74 | 27 | empty |
| 5 | 124 | 0.47 | 0.78 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 391 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 245 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 94 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
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 Q9X2H9
- Elsewhere: RCSB PDB 3HD0 · PDBe 3HD0 · UniProt Q9X2H9
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