Research workbench
Crystal structure of the VMA1-derived endonuclease with the ligated extein segment
Analyse Crystal structure of the VMA1-derived endonuclease with the ligated extein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UM2
- Type
- protein
- Length
- 850 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease pi-scei; 21-mer from vacuolar ATP synthase catalytic subunit a
- EC
- 3.6.3.14
- UniProt
- P17255
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease pi-scei (EC 3.6.3.14) | protein | 417 | 25% helix, 29% strand | P17255 |
| B | Endonuclease pi-scei (EC 3.6.3.14) | protein | 419 | 23% helix, 31% strand | P17255 |
| C, D | 21-mer from vacuolar ATP synthase catalytic subunit a (EC 3.6.3.14) | protein | 7 | 0% helix, 0% strand | P17255 |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.77 | 0.79 | 103 | empty |
| 2 | 459 | 0.65 | 0.78 | 44 | empty |
| 3 | 525 | 0.64 | 0.76 | 59 | empty |
| 4 | 175 | 0.46 | 0.76 | 21 | empty |
| 5 | 172 | 0.45 | 0.75 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1732 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 335 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 331 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1UM2 · Crystal Structure of the Vma1-Derived Endonuclease with the Ligated Extein Segment · the same entry in another collection · chain A against A, TM-score 1.00
- P17255 · AlphaFold monomer V2.0 prediction for V-type proton ATPase catalytic subunit a (P17255) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P17255
- Elsewhere: RCSB PDB 1UM2 · PDBe 1UM2 · UniProt P17255
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