MolNFT v1 · #184766 · protein
Structure of trichophyton rubrum kdnase in complex with 2,3-difluoro- kdn
7P1R · Extracellular SIALIDASE/NEURAMINIDASE: “Structure of trichophyton rubrum kdnase in complex with 2,3-difluoro- kdn”. X-ray diffraction, 3 ligands (FKD, NA, PO4), 14 pockets (best druggability 0.72). MolNFT v1 #184766 on GenesisL1: 3D…
- PDB
- 7P1R
- Type
- protein
- Length
- 1,530 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular SIALIDASE/NEURAMINIDASE
- UniProt
- A0A178EUH2
- Ligands
- FKD, NA, PO4
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Extracellular SIALIDASE/NEURAMINIDASE | protein | 382 | 5% helix, 44% strand | A0A178EUH2 |
| C, D | Extracellular SIALIDASE/NEURAMINIDASE | protein | 383 | 5% helix, 44% strand | A0A178EUH2 |
Ligands and binding sites
- FKD · 3-deoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.72 | 0.78 | 62 | empty |
| 2 | 458 | 0.66 | 0.79 | 41 | empty |
| 3 | 334 | 0.61 | 0.78 | 35 | empty |
| 4 | 308 | 0.60 | 0.78 | 33 | empty |
| 5 | 489 | 0.58 | 0.74 | 45 | empty |
Interfaces
5 interfaces between chains.
- B–D · 453 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 398 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 360 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 122 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 107 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7P1R · Structure of Trichophyton Rubrum KDNase in complex with 2,3-difluoro-KDN · 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 7P1R · PDBe 7P1R · UniProt A0A178EUH2
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