Research workbench
Crystal structure of CGI121/BUD32/KAE1 complex
Analyse Crystal structure of CGI121/BUD32/KAE1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ENH
- Type
- protein
- Length
- 1,256 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative O-sialoglycoprotein endopeptidase; Uncharacterized protein MJ0187
- EC
- 3.4.24.57
- UniProt
- Q58530, Q57646
- Ligands
- TBR
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative O-sialoglycoprotein endopeptidase (EC 3.4.24.57) | protein | 495 | 45% helix, 17% strand | Q58530 |
| B | Putative O-sialoglycoprotein endopeptidase (EC 3.4.24.57) | protein | 485 | 44% helix, 17% strand | Q58530 |
| C, D | Uncharacterized protein MJ0187 | protein | 138 | 41% helix, 12% strand | Q57646 |
Ligands and binding sites
- TBR · Hexatantalum dodecabromide · ligand · 8 copies · chains B, A
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 | 1123 | 0.78 | 0.80 | 108 | empty |
| 2 | 908 | 0.74 | 0.78 | 104 | empty |
| 3 | 334 | 0.58 | 0.77 | 51 | TBR |
| 4 | 286 | 0.52 | 0.74 | 33 | empty |
| 5 | 125 | 0.45 | 0.77 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 752 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 713 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 106 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3ENH · Crystal structure of Cgi121/Bud32/Kae1 complex · 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
- Q57646 · AlphaFold monomer V2.0 prediction for regulatory protein CGI121 (Q57646) · a predicted model of the same protein · chain C 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 Q58530
- Every structure of UniProt Q57646
- Elsewhere: RCSB PDB 3ENH · PDBe 3ENH · UniProt Q58530 · UniProt Q57646
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