Research workbench
Crystal structure analysis of klebsiella sp ASR1 phytase
Analyse Crystal structure analysis of klebsiella sp ASR1 phytase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WNH
- Type
- protein
- Length
- 799 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-phytase
- EC
- 3.1.3.8
- UniProt
- Q84CN9
- Ligands
- NA, MG
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-phytase (EC 3.1.3.8) | protein | 399 | 41% helix, 15% strand | Q84CN9 |
| B | 3-phytase (EC 3.1.3.8) | protein | 400 | 41% helix, 15% strand | Q84CN9 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.74 | 0.88 | 58 | GOL |
| 2 | 475 | 0.68 | 0.79 | 41 | empty |
| 3 | 462 | 0.66 | 0.79 | 42 | empty |
| 4 | 189 | 0.54 | 0.79 | 27 | empty |
| 5 | 137 | 0.48 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1154 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2WNH · Crystal Structure Analysis of Klebsiella sp ASR1 Phytase · 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 Q84CN9
- Elsewhere: RCSB PDB 2WNH · PDBe 2WNH · UniProt Q84CN9
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