Research workbench
The crystal structure of nitrosomonas europaea sucrose synthase: insights into the evolutionary origin of sucrose metabolism in prokaryotes
Analyse The crystal structure of nitrosomonas europaea sucrose synthase: insights into… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RBN
- Type
- protein
- Length
- 3,156 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sucrose SYNTHASE:GLYCOSYL transferases group 1
- EC
- 2.4.1.13
- UniProt
- Q820M5
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B, D | Sucrose SYNTHASE:GLYCOSYL transferases group 1 (EC 2.4.1.13) | protein | 789 | 44% helix, 14% strand | Q820M5 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 905 | 0.82 | 0.84 | 102 | empty |
| 2 | 1063 | 0.82 | 0.83 | 117 | empty |
| 3 | 708 | 0.78 | 0.83 | 76 | empty |
| 4 | 668 | 0.78 | 0.83 | 82 | empty |
| 5 | 831 | 0.76 | 0.80 | 92 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1310 Ų buried · 20 hydrogen bonds · protein-protein
- C–B · 1298 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1259 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1189 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4RBN · The crystal structure of Nitrosomonas europaea sucrose synthase: Insights into the… · the same entry in another collection · chain A against A, TM-score 1.00
- Q820M5 · AlphaFold monomer V2.0 prediction for sucrose synthase (Q820M5) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q820M5
- Elsewhere: RCSB PDB 4RBN · PDBe 4RBN · UniProt Q820M5
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