Research workbench
Enzymatic and structural characterisation of amphinase, a novel cytotoxic ribonuclease from rana pipiens oocytes
Analyse Enzymatic and structural characterisation of amphinase, a novel cytotoxic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P6Z
- Type
- protein
- Length
- 221 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Recombinant amphinase-2
- EC
- 3.1.27.-
- UniProt
- P85073
- Ligands
- NA
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Recombinant amphinase-2 (EC 3.1.27.-) | protein | 112 | 24% helix, 41% strand | P85073 |
| B | Recombinant amphinase-2 (EC 3.1.27.-) | protein | 109 | 22% helix, 42% strand | P85073 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B
- CIT · Citric acid · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.72 | 0.79 | 59 | CIT, NA |
Interfaces
1 interface between chains.
- A–B · 658 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2P6Z · Enzymatic and Structural Characterisation of Amphinase, a Novel Cytotoxic Ribonuclease… · the same entry in another collection · chain A against A, TM-score 1.00
- P85073 · AlphaFold monomer V2.0 prediction for amphinase-2 (P85073) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P85073
- Elsewhere: RCSB PDB 2P6Z · PDBe 2P6Z · UniProt P85073
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