MolNFT v1 · #68677 · protein
Crystal structure of B/PERTH neuraminidase D197E mutant
3K38: “Crystal structure of B/PERTH neuraminidase D197E mutant”. X-ray diffraction, 4 ligands (NAG, YT3, CA), 20 pockets (best druggability 0.83). MolNFT v1 #68677 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3K38
- Type
- protein
- Length
- 6,224 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- EC
- 3.2.1.18
- UniProt
- Q3S340
- Ligands
- NAG, YT3, CA, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P | Neuraminidase (EC 3.2.1.18) | protein | 389 | 2% helix, 48% strand | Q3S340 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- YT3 · Yttrium (III) ion · metal · 20 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- CA · Calcium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
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 | 1096 | 0.83 | 0.84 | 96 | SO4, YT3 |
| 2 | 1012 | 0.80 | 0.81 | 110 | empty |
| 3 | 115 | 0.79 | 0.98 | 25 | empty |
| 4 | 107 | 0.78 | 0.98 | 25 | empty |
| 5 | 106 | 0.78 | 0.98 | 26 | empty |
Interfaces
30 interfaces between chains.
- C–D · 1996 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1988 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1982 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1981 Ų buried · 28 hydrogen bonds · protein-protein
- I–L · 1980 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 128 disulfide, 16 glycan (disulfide, N-glycosylation).
Compared structures
- 3K38 · Crystal Structure of B/Perth Neuraminidase D197E mutant · the same entry in another collection · chain K against K, 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 Q3S340
- Elsewhere: RCSB PDB 3K38 · PDBe 3K38 · UniProt Q3S340
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