Research workbench
Apo structure of kdnase from trichophyton rubrum
Analyse Apo structure of kdnase from trichophyton rubrum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P1V
- Type
- protein
- Length
- 1,533 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular SIALIDASE/NEURAMINIDASE
- UniProt
- A0A178EUH2
- Ligands
- CA
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Extracellular SIALIDASE/NEURAMINIDASE | protein | 384 | 5% helix, 44% strand | A0A178EUH2 |
| C | Extracellular SIALIDASE/NEURAMINIDASE | protein | 381 | 5% helix, 44% strand | A0A178EUH2 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.74 | 0.77 | 94 | empty |
| 2 | 966 | 0.74 | 0.77 | 73 | empty |
| 3 | 590 | 0.62 | 0.74 | 49 | empty |
| 4 | 332 | 0.62 | 0.79 | 33 | empty |
| 5 | 331 | 0.61 | 0.78 | 31 | empty |
Interfaces
5 interfaces between chains.
- B–D · 447 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 357 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 351 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 125 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 101 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7P1V · Apo structure of KDNase from Trichophyton Rubrum · 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 A0A178EUH2
- Elsewhere: RCSB PDB 7P1V · PDBe 7P1V · UniProt A0A178EUH2
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