Research workbench
Structure of the archaeal KAE1-BUD32 fusion protein MJ1130: a model for the eukaryotic ekc-keops subcomplex involved in transcription and telomere homeostasis.
Analyse Structure of the archaeal KAE1-BUD32 fusion protein MJ1130: a model for the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VWB
- Type
- protein
- Length
- 1,026 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative O-sialoglycoprotein endopeptidase
- EC
- 3.4.24.57
- UniProt
- Q58530
- Ligands
- ANP
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative O-sialoglycoprotein endopeptidase (EC 3.4.24.57) | protein | 519 | 44% helix, 20% strand | Q58530 |
| B | Putative O-sialoglycoprotein endopeptidase (EC 3.4.24.57) | protein | 507 | 48% helix, 19% strand | Q58530 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1012 | 0.80 | 0.81 | 105 | empty |
| 2 | 747 | 0.78 | 0.82 | 94 | empty |
| 3 | 290 | 0.63 | 0.80 | 40 | ANP |
| 4 | 192 | 0.60 | 0.82 | 35 | ANP |
| 5 | 135 | 0.51 | 0.80 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 477 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2VWB · Structure of the archaeal Kae1-Bud32 fusion protein MJ1130: a model for the eukaryotic… · the same entry in another collection · chain A against A, TM-score 1.00
- Q58530 · AlphaFold monomer V2.0 prediction for probable bifunctional tRNA… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q58530
- Elsewhere: RCSB PDB 2VWB · PDBe 2VWB · UniProt Q58530
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