MolNFT v1 · #176487 · protein
Crystal structure of a nuclease and capping domain of sbcd from staphylococcus aureus
7DOG · Nuclease sbccd subunit D: “Crystal structure of a nuclease and capping domain of sbcd from staphylococcus aureus”. X-ray diffraction, 1 ligand (MN), 1 pocket (best druggability 0.50). MolNFT v1 #176487 on GenesisL1: 3D structure…
- PDB
- 7DOG
- Type
- protein
- Length
- 638 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclease sbccd subunit D
- UniProt
- Q99UD1
- Ligands
- MN
- Pockets
- 1 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclease sbccd subunit D | protein | 319 | 28% helix, 27% strand | Q99UD1 |
| B | Nuclease sbccd subunit D | protein | 319 | 27% helix, 26% strand | Q99UD1 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.50 | 0.86 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1150 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7DOG · Crystal structure of a nuclease and capping domain of SbcD from Staphylococcus aureus · the same entry in another collection · chain A against A, TM-score 1.00
- Q99UD1 · AlphaFold monomer V2.0 prediction for nuclease sbccd subunit D (Q99UD1) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q99UD1
- Elsewhere: RCSB PDB 7DOG · PDBe 7DOG · UniProt Q99UD1
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