Research workbench
Crystal structure of the giy-yig N-terminal endonuclease domain of uvrc from bacillus caldotenax
Analyse Crystal structure of the giy-yig N-terminal endonuclease domain of uvrc from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YD6
- Type
- protein
- Length
- 373 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uvrc
- Ligands
- CL, SO4
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uvrc | protein | 95 | 48% helix, 20% strand | — |
| B | Uvrc | protein | 88 | 44% helix, 22% strand | — |
| C | Uvrc | protein | 94 | 47% helix, 20% strand | — |
| D | Uvrc | protein | 96 | 46% helix, 20% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.66 | 0.76 | 58 | CL, SO4 |
| 2 | 70 | 0.44 | 0.81 | 18 | empty |
| 3 | 190 | 0.43 | 0.73 | 36 | empty |
| 4 | 75 | 0.32 | 0.74 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 417 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 412 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 365 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 343 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 20 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1YD6 · Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Bacillus… · 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
- Elsewhere: RCSB PDB 1YD6 · PDBe 1YD6
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