MolNFT v1 · #119945 · protein
Structure of PL6 family alginate lyase alygc
5GKD: “Structure of PL6 family alginate lyase alygc”. X-ray diffraction, 3 ligands (CA, PO4, CO3), 15 pockets (best druggability 0.86). MolNFT v1 #119945 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GKD
- Type
- protein
- Length
- 2,904 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alygc
- Ligands
- CA, PO4, CO3
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Alygc | protein | 726 | 4% helix, 44% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 12 copies · chains A, D, B, C
- CO3 · Carbonate ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 16 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1115 | 0.86 | 0.87 | 165 | GOL, PO4, CO3 |
| 2 | 309 | 0.61 | 0.79 | 39 | empty |
| 3 | 320 | 0.61 | 0.78 | 37 | empty |
| 4 | 322 | 0.60 | 0.78 | 40 | empty |
| 5 | 295 | 0.60 | 0.79 | 37 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1092 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 313 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 143 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 40 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 39 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5GKD · Structure of PL6 family alginate lyase AlyGC · 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
- Elsewhere: RCSB PDB 5GKD · PDBe 5GKD
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.