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
- 7LCE
- Type
- protein
- Length
- 1,476 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-glucosaminate-6-phosphate ammonia lyase
- EC
- 2.9.1.1
- UniProt
- A0A0D6I3R5
- Ligands
- CA
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | D-glucosaminate-6-phosphate ammonia lyase (EC 2.9.1.1) | protein | 369 | 45% helix, 18% strand | A0A0D6I3R5 |
Ligands and binding sites
- CA · Calcium ion · metal · 16 copies · chains A, D, B, C
- DMS · Dimethyl sulfoxide · additive · 6 copies · chains A, B, C, 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 | 1162 | 0.74 | 0.77 | 123 | empty |
| 2 | 814 | 0.71 | 0.77 | 66 | DMS |
| 3 | 854 | 0.70 | 0.76 | 80 | empty |
| 4 | 281 | 0.69 | 0.84 | 41 | empty |
| 5 | 790 | 0.68 | 0.75 | 71 | empty |
Interfaces
5 interfaces between chains.
- A–D · 3228 Ų buried · 44 hydrogen bonds · protein-protein
- B–D · 640 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 606 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 141 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 140 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 7LCE · 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 A0A0D6I3R5
- Elsewhere: RCSB PDB 7LCE · PDBe 7LCE · UniProt A0A0D6I3R5
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