Research workbench
Crystal structure of endo-neuraminidase nf mutant
Analyse Crystal structure of endo-neuraminidase nf mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GVK
- Type
- protein
- Length
- 1,976 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-N-acetylneuraminidase
- EC
- 3.2.1.129
- UniProt
- Q858B1
- Ligands
- SIA, SLB, NA
- Pockets
- 19 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-N-acetylneuraminidase (EC 3.2.1.129) | protein | 644 | 2% helix, 44% strand | Q858B1 |
| B, C | Endo-N-acetylneuraminidase (EC 3.2.1.129) | protein | 666 | 3% helix, 43% strand | Q858B1 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 15 copies · chains A, C, B
- SLB · N-acetyl-beta-neuraminic acid · sugar · 9 copies · chains A, B, C
- NA · Sodium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.89 | 0.91 | 180 | empty |
| 2 | 1169 | 0.83 | 0.84 | 129 | empty |
| 3 | 82 | 0.78 | 0.98 | 18 | empty |
| 4 | 127 | 0.67 | 0.89 | 27 | empty |
| 5 | 301 | 0.56 | 0.76 | 32 | SLB |
Interfaces
3 interfaces between chains.
- B–C · 7471 Ų buried · 141 hydrogen bonds · protein-protein
- A–C · 7440 Ų buried · 146 hydrogen bonds · protein-protein
- A–B · 7377 Ų buried · 149 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 glycan (glycosylation).
Compared structures
- 3GVK · Crystal structure of endo-neuraminidase NF mutant · 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 Q858B1
- Elsewhere: RCSB PDB 3GVK · PDBe 3GVK · UniProt Q858B1
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