MolNFT v1 · #109253 · protein
Crystal structure of binary complex GON7-PCC1
4WX8 · EKC/KEOPS complex subunit PCC1: “Crystal structure of binary complex GON7-PCC1”. X-ray diffraction, 2 pockets (best druggability 0.59). MolNFT v1 #109253 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4WX8
- Type
- protein
- Length
- 423 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EKC/KEOPS complex subunit PCC1; EKC/KEOPS complex subunit GON7
- UniProt
- Q3E833, P46984
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 6 distinct chains · 51% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | EKC/KEOPS complex subunit PCC1 | protein | 83 | 46% helix, 29% strand | Q3E833 |
| B | EKC/KEOPS complex subunit PCC1 | protein | 84 | 44% helix, 29% strand | Q3E833 |
| C | EKC/KEOPS complex subunit PCC1 | protein | 81 | 47% helix, 30% strand | Q3E833 |
| D | EKC/KEOPS complex subunit GON7 | protein | 64 | 58% helix, 16% strand | P46984 |
| E | EKC/KEOPS complex subunit GON7 | protein | 61 | 61% helix, 15% strand | P46984 |
| F | EKC/KEOPS complex subunit GON7 | protein | 50 | 56% helix, 20% strand | P46984 |
Ligands and binding sites
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 386 | 0.59 | 0.76 | 56 | empty |
| 2 | 193 | 0.54 | 0.78 | 24 | empty |
Interfaces
6 interfaces between chains.
- B–E · 1166 Ų buried · 19 hydrogen bonds · protein-protein
- C–F · 997 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 423 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 409 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 349 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 4WX8 · Crystal structure of binary complex Gon7-Pcc1 · the same entry in another collection · chain F against F, TM-score 1.00
- P46984 · AlphaFold monomer V2.0 prediction for EKC/KEOPS complex subunit GON7 (P46984) · a predicted model of the same protein · chain F against A, TM-score 0.94
- Q3E833 · AlphaFold monomer V2.0 prediction for EKC/KEOPS complex subunit PCC1 (Q3E833) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 Q3E833
- Every structure of UniProt P46984
- Elsewhere: RCSB PDB 4WX8 · PDBe 4WX8 · UniProt Q3E833 · UniProt P46984
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