MolNFT v1 · #74080 · protein
Crystal structure of B. megaterium levansucrase mutant Y247W
3OM7: “Crystal structure of B. megaterium levansucrase mutant Y247W”. X-ray diffraction, 2 ligands (CA, SO4), 13 pockets (best druggability 0.74). MolNFT v1 #74080 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3OM7
- 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
- 13 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, B, D | Levansucrase (EC 2.4.1.10) | protein | 448 | 15% helix, 43% strand | D5DC07 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains C, A, B, D
- SO4 · Sulfate ion · ion · 7 copies · chains C, A, B, D
- PGE · Triethylene glycol · additive · 4 copies · chains C, A, B, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 745 | 0.74 | 0.80 | 76 | SO4 |
| 2 | 459 | 0.67 | 0.79 | 45 | empty |
| 3 | 406 | 0.60 | 0.76 | 41 | PEG, PGE |
| 4 | 347 | 0.59 | 0.77 | 41 | PGE, PEG |
| 5 | 351 | 0.58 | 0.76 | 49 | PGE, PEG |
Interfaces
3 interfaces between chains.
- A–B · 805 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 799 Ų buried · 19 hydrogen bonds · protein-protein
- C–A · 490 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3OM7 · Crystal structure of B. megaterium levansucrase mutant Y247W · the same entry in another collection · chain C against C, 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 3OM7 · PDBe 3OM7 · UniProt D5DC07
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