Research workbench
Phage PHI92 endosialidase
Analyse Phage PHI92 endosialidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HIZ
- Type
- protein
- Length
- 1,965 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endosialidase
- EC
- 3.2.1.129
- UniProt
- I7HXG2
- Ligands
- SLB, SIA, GLC, FRU, NA, CA, MG, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endosialidase (EC 3.2.1.129) | protein | 658 | 3% helix, 45% strand | I7HXG2 |
| B | Endosialidase (EC 3.2.1.129) | protein | 652 | 3% helix, 44% strand | I7HXG2 |
| C | Endosialidase (EC 3.2.1.129) | protein | 655 | 3% helix, 45% strand | I7HXG2 |
Ligands and binding sites
- SLB · N-acetyl-beta-neuraminic acid · sugar · 3 copies · chains A, B, C
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, C, B
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains A, B, C
- FRU · beta-D-fructofuranose · sugar · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 12 copies · chains A, B, C
- CA · Calcium ion · metal · 6 copies · chains A, B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 43 copies · chains A, B, 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.87 | 0.88 | 171 | EDO, NA |
| 2 | 94 | 0.80 | 1.00 | 24 | empty |
| 3 | 278 | 0.68 | 0.84 | 41 | empty |
| 4 | 274 | 0.56 | 0.77 | 25 | EDO, NA |
| 5 | 283 | 0.55 | 0.76 | 27 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 7432 Ų buried · 136 hydrogen bonds · protein-protein
- A–C · 7424 Ų buried · 136 hydrogen bonds · protein-protein
- B–C · 7393 Ų buried · 135 hydrogen bonds · protein-protein
Compared structures
- 4HIZ · Phage phi92 endosialidase · 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 I7HXG2
- Elsewhere: RCSB PDB 4HIZ · PDBe 4HIZ · UniProt I7HXG2
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