Research workbench
Structure of D-Glucosaminate-6-phosphate Ammonia-lyase
Analyse Structure of D-Glucosaminate-6-phosphate Ammonia-lyase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LC0
- Type
- protein
- Length
- 2,952 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
- Molecule
- Putative selenocysteine synthase (L-seryl-tRNA(Ser) selenium transferase)
- UniProt
- Q8ZL27
- Ligands
- MG, CL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.6 · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Putative selenocysteine synthase (L-seryl-tRNA(Ser) selenium transferase) | protein | 369 | 44% helix, 17% strand | Q8ZL27 |
Ligands and binding sites
- MG · Magnesium ion · metal · 11 copies · chains A, B, C, E, F, G, H
- CL · Chloride ion · ion · chains B, H
- DMS · Dimethyl sulfoxide · additive · 19 copies · chains A, B, C, D, F, E, G
- ACY · Acetic acid · additive · 5 copies · chains A, B, C, E, G, F
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.78 | 0.80 | 107 | empty |
| 2 | 675 | 0.73 | 0.80 | 74 | ACY |
| 3 | 891 | 0.71 | 0.76 | 86 | empty |
| 4 | 649 | 0.71 | 0.78 | 62 | empty |
| 5 | 234 | 0.70 | 0.86 | 42 | empty |
Interfaces
16 interfaces between chains.
- B–C · 3279 Ų buried · 40 hydrogen bonds · protein-protein
- E–G · 3272 Ų buried · 40 hydrogen bonds · protein-protein
- D–F · 3267 Ų buried · 48 hydrogen bonds · protein-protein
- A–H · 3249 Ų buried · 42 hydrogen bonds · protein-protein
- B–H · 608 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 96 modified (engineered, cofactor).
Compared structures
- 7LC0 · Structure of D-glucosaminate-6-phosphate ammonia-lyase · 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 Q8ZL27
- Elsewhere: RCSB PDB 7LC0 · PDBe 7LC0 · UniProt Q8ZL27
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