Research workbench
Crystal structure of B. megaterium levansucrase mutant N252A
Analyse Crystal structure of B. megaterium levansucrase mutant N252A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OM5
- Type
- protein
- Length
- 1,792 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Levansucrase
- EC
- 2.4.1.10
- UniProt
- D5DC07
- Ligands
- CA, SO4
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Levansucrase (EC 2.4.1.10) | protein | 448 | 15% helix, 41% strand | D5DC07 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains C, D
- P6G · Hexaethylene glycol · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains C
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 748 | 0.74 | 0.80 | 82 | SO4 |
| 2 | 652 | 0.73 | 0.80 | 58 | empty |
| 3 | 891 | 0.71 | 0.76 | 91 | P6G |
| 4 | 761 | 0.70 | 0.77 | 90 | SO4 |
| 5 | 357 | 0.57 | 0.75 | 43 | PEG |
Interfaces
4 interfaces between chains.
- A–C · 828 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 801 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 505 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 466 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3OM5 · Crystal structure of B. megaterium levansucrase mutant N252A · 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 D5DC07
- Elsewhere: RCSB PDB 3OM5 · PDBe 3OM5 · UniProt D5DC07
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