Research workbench
Crystal structure of binary complex GON7-PCC1
Analyse Crystal structure of binary complex GON7-PCC1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WXA
- Type
- protein
- Length
- 432 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 0.58
Structure
x-ray diffraction · 5 distinct chains · 52% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | EKC/KEOPS complex subunit PCC1 | protein | 84 | 43% helix, 29% strand | Q3E833 |
| C | EKC/KEOPS complex subunit PCC1 | protein | 78 | 41% helix, 31% strand | Q3E833 |
| D | EKC/KEOPS complex subunit GON7 | protein | 68 | 62% helix, 15% strand | P46984 |
| E | EKC/KEOPS complex subunit GON7 | protein | 69 | 62% helix, 16% strand | P46984 |
| F | EKC/KEOPS complex subunit GON7 | protein | 49 | 57% helix, 22% strand | P46984 |
Ligands and binding sites
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 | 352 | 0.58 | 0.76 | 41 | empty |
| 2 | 212 | 0.55 | 0.78 | 27 | empty |
Interfaces
6 interfaces between chains.
- B–E · 1206 Ų buried · 18 hydrogen bonds · protein-protein
- C–F · 1143 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 369 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 363 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 350 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 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 0.96
- 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 4WXA · PDBe 4WXA · UniProt Q3E833 · UniProt P46984
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