MolNFT v1 · #74077 · protein
Crystal structure of B. megaterium levansucrase mutant K373A
3OM4: “Crystal structure of B. megaterium levansucrase mutant K373A”. X-ray diffraction, 2 ligands (CA, SO4), 13 pockets (best druggability 0.74). MolNFT v1 #74077 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3OM4
- 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, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Levansucrase (EC 2.4.1.10) | protein | 448 | 15% helix, 44% strand | D5DC07 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 5 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.74 | 0.80 | 56 | empty |
| 2 | 713 | 0.73 | 0.79 | 85 | SO4 |
| 3 | 630 | 0.67 | 0.76 | 78 | empty |
| 4 | 367 | 0.58 | 0.76 | 45 | PGE |
| 5 | 355 | 0.58 | 0.76 | 36 | PEG, PGE |
Interfaces
4 interfaces between chains.
- A–B · 819 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 805 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 519 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 432 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3OM4 · Crystal structure of B. megaterium levansucrase mutant K373A · 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 3OM4 · PDBe 3OM4 · UniProt D5DC07
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