MolNFT v1 · #121708 · protein
Crystal structure of putative putative deoxyribonuclease-2 from burkholderia thailandensis, E264
5I3E: “Crystal structure of putative putative deoxyribonuclease-2 from burkholderia thailandensis, E264”. X-ray diffraction, 6 pockets (best druggability 0.66). MolNFT v1 #121708 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5I3E
- Type
- protein
- Length
- 694 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative deoxyribonuclease-2
- EC
- 3.1.-.-
- UniProt
- Q2T8B0
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative deoxyribonuclease-2 (EC 3.1.-.-) | protein | 346 | 19% helix, 29% strand | Q2T8B0 |
| B | Putative deoxyribonuclease-2 (EC 3.1.-.-) | protein | 348 | 18% helix, 29% strand | Q2T8B0 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
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 | 536 | 0.66 | 0.77 | 69 | empty |
| 2 | 134 | 0.51 | 0.80 | 20 | empty |
| 3 | 175 | 0.48 | 0.76 | 24 | empty |
| 4 | 75 | 0.47 | 0.82 | 21 | empty |
| 5 | 104 | 0.47 | 0.80 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1371 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5I3E · Crystal structure of putative Putative deoxyribonuclease-2 from Burkholderia… · the same entry in another collection · chain B against B, TM-score 1.00
- Q2T8B0 · AlphaFold monomer V2.0 prediction for putative deoxyribonuclease-2 (Q2T8B0) · a predicted model of the same protein · chain B against A, TM-score 0.86
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 Q2T8B0
- Elsewhere: RCSB PDB 5I3E · PDBe 5I3E · UniProt Q2T8B0
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