MolNFT v1 · #109222 · protein
Crystal structure of binary complex BUD32-CGI121 in complex with ADP
4WW9 · EKC/KEOPS complex subunit BUD32: “Crystal structure of binary complex BUD32-CGI121 in complex with ADP”. X-ray diffraction, 3 ligands (ADP, MG, SO4), 6 pockets (best druggability 0.59). MolNFT v1 #109222 on GenesisL1: 3D structure…
- PDB
- 4WW9
- Type
- protein
- Length
- 415 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EKC/KEOPS complex subunit BUD32; EKC/KEOPS complex subunit CGI121
- EC
- 3.6.-.-, 2.7.11.1
- UniProt
- P53323, Q03705
- Ligands
- ADP, MG, SO4
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | EKC/KEOPS complex subunit BUD32 (EC 3.6.-.-, 2.7.11.1) | protein | 238 | 44% helix, 19% strand | P53323 |
| B | EKC/KEOPS complex subunit CGI121 | protein | 177 | 46% helix, 18% strand | Q03705 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.59 | 0.81 | 31 | MG, ADP |
| 2 | 259 | 0.52 | 0.75 | 43 | empty |
| 3 | 118 | 0.43 | 0.77 | 18 | empty |
| 4 | 55 | 0.35 | 0.79 | 14 | empty |
| 5 | 62 | 0.30 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1218 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4WW9 · Crystal structure of binary complex Bud32-Cgi121 in complex with ADP · the same entry in another collection · chain A against A, TM-score 1.00
- Q03705 · AlphaFold monomer V2.0 prediction for EKC/KEOPS complex subunit CGI121 (Q03705) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P53323 · AlphaFold monomer V2.0 prediction for EKC/KEOPS complex subunit BUD32 (P53323) · 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 P53323
- Every structure of UniProt Q03705
- Elsewhere: RCSB PDB 4WW9 · PDBe 4WW9 · UniProt P53323 · UniProt Q03705
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