MolNFT v1 · #168781 · protein
Human prpk-tprkb complex
6WQX · EKC/KEOPS complex subunit tprkb: “Human prpk-tprkb complex”. X-ray diffraction, 2 ligands (ANP, MG), 13 pockets (best druggability 0.63). MolNFT v1 #168781 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6WQX
- Type
- protein
- Length
- 811 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EKC/KEOPS complex subunit tprkb; EKC/KEOPS complex subunit TP53RK
- EC
- 3.6.-.-, 2.7.11.1
- UniProt
- Q9Y3C4, Q96S44
- Ligands
- ANP, MG
- Pockets
- 13 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | EKC/KEOPS complex subunit tprkb | protein | 175 | 49% helix, 17% strand | Q9Y3C4 |
| C | EKC/KEOPS complex subunit TP53RK (EC 3.6.-.-, 2.7.11.1) | protein | 231 | 51% helix, 18% strand | Q96S44 |
| D | EKC/KEOPS complex subunit TP53RK (EC 3.6.-.-, 2.7.11.1) | protein | 230 | 52% helix, 20% strand | Q96S44 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains C, D
- MG · Magnesium ion · metal · 3 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.63 | 0.79 | 34 | ANP, MG |
| 2 | 329 | 0.61 | 0.78 | 35 | ANP, MG |
| 3 | 401 | 0.58 | 0.75 | 34 | empty |
| 4 | 163 | 0.54 | 0.80 | 19 | empty |
| 5 | 126 | 0.49 | 0.79 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1439 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1394 Ų buried · 11 hydrogen bonds · protein-protein
- B–A · 275 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6WQX · Human PRPK-TPRKB complex · the same entry in another collection · chain B against B, TM-score 1.00
- Q9Y3C4 · AlphaFold monomer V2.0 prediction for EKC/KEOPS complex subunit tprkb (Q9Y3C4) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q96S44 · AlphaFold monomer V2.0 prediction for EKC/KEOPS complex subunit TP53RK (Q96S44) · a predicted model of the same protein · chain C 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 Q9Y3C4
- Every structure of UniProt Q96S44
- Elsewhere: RCSB PDB 6WQX · PDBe 6WQX · UniProt Q9Y3C4 · UniProt Q96S44
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