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Crystal structure of a putative hd superfamily hydrolase (BH1327) from bacillus halodurans at 1.90 a resolution
Analyse Crystal structure of a putative hd superfamily hydrolase (BH1327) from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O08
- Type
- protein
- Length
- 374 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BH1327 protein
- UniProt
- Q9KD90
- Ligands
- UNL, DGI, FE, PO4, NO3
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | BH1327 protein | protein | 187 | 71% helix, 0% strand | Q9KD90 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · chains A
- DGI · 2'-deoxyguanosine-5'-diphosphate · ligand · chains B
- FE · Fe (III) ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
- NO3 · Nitrate ion · ion · chains B
- PG4 · Tetraethylene glycol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.65 | 0.80 | 30 | FE, DGI |
| 2 | 276 | 0.58 | 0.78 | 30 | FE, PO4, UNL |
| 3 | 88 | 0.48 | 0.81 | 21 | empty |
| 4 | 54 | 0.43 | 0.83 | 15 | empty |
| 5 | 56 | 0.40 | 0.80 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 731 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2O08 · Crystal structure of a putative hd superfamily hydrolase (BH1327) 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
- Every structure of UniProt Q9KD90
- Elsewhere: RCSB PDB 2O08 · PDBe 2O08 · UniProt Q9KD90
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