Research workbench
Crystal structure of a protein member of the UPF0052 family (BH3568) from bacillus halodurans at 2.60 a resolution
Analyse Crystal structure of a protein member of the UPF0052 family (BH3568) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O2Z
- Type
- protein
- Length
- 1,237 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- UniProt
- Q9K706
- Ligands
- NAD, SO4
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein | protein | 310 | 41% helix, 20% strand | Q9K706 |
| B | Hypothetical protein | protein | 308 | 40% helix, 20% strand | Q9K706 |
| C | Hypothetical protein | protein | 309 | 41% helix, 20% strand | Q9K706 |
| D | Hypothetical protein | protein | 310 | 41% helix, 20% strand | Q9K706 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.73 | 0.89 | 20 | empty |
| 2 | 174 | 0.71 | 0.88 | 22 | empty |
| 3 | 308 | 0.64 | 0.81 | 38 | SO4, NAD |
| 4 | 355 | 0.63 | 0.79 | 42 | SO4, NAD |
| 5 | 326 | 0.62 | 0.79 | 32 | SO4, NAD |
Interfaces
3 interfaces between chains.
- C–D · 1158 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 1129 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 563 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 2O2Z · Crystal structure of a protein member of the upf0052 family (bh3568) from bacillus… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9K706 · AlphaFold monomer V2.0 prediction for gluconeogenesis factor (Q9K706) · a predicted model of the same protein · chain C 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
- Every structure of UniProt Q9K706
- Elsewhere: RCSB PDB 2O2Z · PDBe 2O2Z · UniProt Q9K706
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