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Crystal structure of a 6-phosphogluconolactonase (SBAL_2240) from shewanella baltica OS155 at 1.40 a resolution
Analyse Crystal structure of a 6-phosphogluconolactonase (SBAL_2240) from shewanella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NWP
- Type
- protein
- Length
- 466 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phosphogluconolactonase
- UniProt
- B8E528
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 6-phosphogluconolactonase | protein | 233 | 36% helix, 20% strand | B8E528 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
- P6G · Hexaethylene glycol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.70 | 0.87 | 39 | empty |
| 2 | 152 | 0.57 | 0.82 | 29 | empty |
| 3 | 141 | 0.53 | 0.81 | 22 | empty |
| 4 | 50 | 0.41 | 0.83 | 18 | GOL |
Interfaces
1 interface between chains.
- A–B · 491 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3NWP · Crystal structure of a 6-phosphogluconolactonase (Sbal_2240) from Shewanella baltica… · 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 B8E528
- Elsewhere: RCSB PDB 3NWP · PDBe 3NWP · UniProt B8E528
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