Research workbench
Influenza virus neuraminidase subtype N9 (tern) with tetrabrachion (tb) domain stalk
Analyse Influenza virus neuraminidase subtype N9 (tern) with tetrabrachion (tb) domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CRD
- Type
- protein
- Length
- 3,492 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TETRABRACHION,NEURAMINIDASE
- EC
- 3.2.1.18
- UniProt
- Q54436, P03472
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F | TETRABRACHION,NEURAMINIDASE (EC 3.2.1.18) | protein | 438 | 13% helix, 39% strand | Q54436, P03472 |
| C, D, G, H | TETRABRACHION,NEURAMINIDASE (EC 3.2.1.18) | protein | 435 | 11% helix, 39% strand | Q54436, P03472 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 54 copies · chains A, B, E, C, D, G, H, F
- MAN · alpha-D-mannopyranose · sugar · 49 copies · chains B, E, D, G, H, C, F, A
- BMA · beta-D-mannopyranose · sugar · 9 copies · chains B, E, D, G, H, C, F, A
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 | 133 | 0.82 | 0.98 | 16 | empty |
| 2 | 136 | 0.81 | 0.97 | 18 | empty |
| 3 | 127 | 0.81 | 0.98 | 19 | empty |
| 4 | 89 | 0.78 | 0.98 | 16 | empty |
| 5 | 121 | 0.76 | 0.95 | 20 | empty |
Interfaces
13 interfaces between chains.
- C–F · 2744 Ų buried · 30 hydrogen bonds · protein-protein
- F–G · 2729 Ų buried · 29 hydrogen bonds · protein-protein
- E–H · 2706 Ų buried · 39 hydrogen bonds · protein-protein
- B–E · 2705 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2698 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 disulfide, 31 glycan (disulfide, N-glycosylation).
Compared structures
- 6CRD · INFLUENZA VIRUS NEURAMINIDASE SUBTYPE N9 (TERN) with tetrabrachion (TB) domain stalk · 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 Q54436
- Every structure of UniProt P03472
- Elsewhere: RCSB PDB 6CRD · PDBe 6CRD · UniProt Q54436 · UniProt P03472
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