Research workbench
ATXE2 isopeptidase - S527A variant with ASTEXIN3-DC4 bound
Analyse ATXE2 isopeptidase - S527A variant with ASTEXIN3-DC4 bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TXE
- Type
- protein
- Length
- 1,339 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATXE2; ASTEXIN3-DC4
- UniProt
- E8RUP5, E8RUP8
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ATXE2 | protein | 652 | 26% helix, 33% strand | E8RUP5 |
| C | ASTEXIN3-DC4 | protein | 17 | 0% helix, 24% strand | E8RUP8 |
| D | ASTEXIN3-DC4 | protein | 18 | 0% helix, 22% strand | E8RUP8 |
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 726 | 0.82 | 0.86 | 83 | empty |
| 2 | 783 | 0.81 | 0.84 | 88 | empty |
| 3 | 624 | 0.71 | 0.79 | 62 | empty |
| 4 | 434 | 0.68 | 0.80 | 36 | empty |
| 5 | 340 | 0.67 | 0.81 | 49 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1616 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1087 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1035 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5TXE · AtxE2 Isopeptidase - S527A Variant with Astexin3-dC4 Bound · the same entry in another collection · chain D against D, TM-score 1.00
- E8RUP5 · AlphaFold monomer V2.0 prediction for lasso peptide isopeptidase ATXE2 (E8RUP5) · a predicted model of the same protein · chain B against A, TM-score 1.00
- E8RUP8 · AlphaFold monomer V2.0 prediction for astexin-3 (E8RUP8) · a predicted model of the same protein · chain C against A, TM-score 0.21
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 E8RUP5
- Every structure of UniProt E8RUP8
- Elsewhere: RCSB PDB 5TXE · PDBe 5TXE · UniProt E8RUP5 · UniProt E8RUP8
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