MolNFT v1 · #47245 · protein + DNA
The structure of a bacterial homing endonuclease : I-SSP6803I
2OST · Synthetic DNA 29 mer: “The structure of a bacterial homing endonuclease : I-SSP6803I”. X-ray diffraction, 1 ligand (CA), 12 pockets (best druggability 0.81). MolNFT v1 #47245 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2OST
- Type
- protein + DNA
- Length
- 625 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Synthetic DNA 29 mer; Putative endonuclease
- UniProt
- Q57253
- Ligands
- CA
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 27% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Y | Synthetic DNA 29 mer | dna | 29 | — | — |
| Z | Synthetic DNA 29 mer | dna | 29 | — | — |
| A | Putative endonuclease | protein | 148 | 22% helix, 34% strand | Q57253 |
| B | Putative endonuclease | protein | 148 | 28% helix, 35% strand | Q57253 |
| C | Putative endonuclease | protein | 138 | 29% helix, 28% strand | Q57253 |
| D | Putative endonuclease | protein | 133 | 28% helix, 32% strand | Q57253 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains Y, A, Z, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.81 | 0.83 | 102 | empty |
| 2 | 280 | 0.55 | 0.76 | 23 | empty |
| 3 | 203 | 0.51 | 0.77 | 25 | empty |
| 4 | 155 | 0.51 | 0.79 | 14 | empty |
| 5 | 67 | 0.49 | 0.84 | 17 | empty |
Interfaces
11 interfaces between chains.
- Y–Z · 1322 Ų buried · 139 hydrogen bonds · nucleic-nucleic
- Y–A · 1187 Ų buried · 23 hydrogen bonds · protein-nucleic
- Z–B · 1117 Ų buried · 17 hydrogen bonds · protein-nucleic
- Z–A · 936 Ų buried · 22 hydrogen bonds · protein-nucleic
- Y–B · 783 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 2OST · The structure of a bacterial homing endonuclease : I-Ssp6803I · the same entry in another collection · chain Y against Y, 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 Q57253
- Elsewhere: RCSB PDB 2OST · PDBe 2OST · UniProt Q57253
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