MolNFT v1 · #45935 · protein
CLP1-ATP-PCF11 complex
2NPI · Protein CLP1: “CLP1-ATP-PCF11 complex”. X-ray diffraction, 2 ligands (ATP, MG), 9 pockets (best druggability 0.83). MolNFT v1 #45935 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2NPI
- Type
- protein
- Length
- 903 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein CLP1; Protein PCF11
- UniProt
- Q08685, P39081
- Ligands
- ATP, MG
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein CLP1 | protein | 428 | 26% helix, 26% strand | Q08685 |
| C | Protein PCF11 | protein | 22 | 27% helix, 9% strand | P39081 |
| D | Protein PCF11 | protein | 25 | 24% helix, 4% strand | P39081 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.83 | 0.91 | 51 | MG, ATP |
| 2 | 412 | 0.82 | 0.91 | 60 | MG, ATP |
| 3 | 555 | 0.77 | 0.84 | 50 | empty |
| 4 | 147 | 0.52 | 0.80 | 20 | empty |
| 5 | 134 | 0.50 | 0.80 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1643 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1604 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 974 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2NPI · Clp1-ATP-Pcf11 complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q08685 · AlphaFold monomer V2.0 prediction for mRNA cleavage and polyadenylation factor CLP1… · a predicted model of the same protein · chain A against A, TM-score 0.98
- P39081 · AlphaFold monomer V2.0 prediction for protein PCF11 (P39081) · a predicted model of the same protein · chain D against A, TM-score 0.48
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 Q08685
- Every structure of UniProt P39081
- Elsewhere: RCSB PDB 2NPI · PDBe 2NPI · UniProt Q08685 · UniProt P39081
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