Research workbench
Crystal structure of the ectoine synthase from the cold-adapted marine bacterium sphingopyxis alaskensis
Analyse Crystal structure of the ectoine synthase from the cold-adapted marine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BXX
- Type
- protein
- Length
- 457 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-ectoine synthase
- EC
- 4.2.1.108
- UniProt
- Q1GNW6
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-ectoine synthase (EC 4.2.1.108) | protein | 121 | 7% helix, 52% strand | Q1GNW6 |
| B | L-ectoine synthase (EC 4.2.1.108) | protein | 113 | 6% helix, 54% strand | Q1GNW6 |
| C | L-ectoine synthase (EC 4.2.1.108) | protein | 111 | 6% helix, 54% strand | Q1GNW6 |
| D | L-ectoine synthase (EC 4.2.1.108) | protein | 112 | 6% helix, 54% strand | Q1GNW6 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.76 | 0.98 | 24 | empty |
| 2 | 107 | 0.50 | 0.81 | 20 | empty |
| 3 | 111 | 0.50 | 0.80 | 20 | empty |
| 4 | 77 | 0.50 | 0.83 | 18 | empty |
| 5 | 131 | 0.40 | 0.74 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1484 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1444 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 292 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 25 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5BXX · Crystal structure of the ectoine synthase from the cold-adapted marine bacterium… · the same entry in another collection · chain D against D, TM-score 1.00
- Q1GNW6 · AlphaFold monomer V2.0 prediction for L-ectoine synthase (Q1GNW6) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q1GNW6
- Elsewhere: RCSB PDB 5BXX · PDBe 5BXX · UniProt Q1GNW6
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