MolNFT v1 · #87405 · protein
Structure of wild-type CLP1P-PCF11P (454 -563) complex
4C0B · MRNA cleavage and polyadenylation factor CLP1: “Structure of wild-type CLP1P-PCF11P (454 -563) complex”. X-ray diffraction, 2 ligands (ATP, MG), 6 pockets (best druggability 0.84). MolNFT v1 #87405 on GenesisL1: 3D structure…
- PDB
- 4C0B
- Type
- protein
- Length
- 921 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA cleavage and polyadenylation factor CLP1; PCF11P
- UniProt
- Q08685, N1P6M1
- Ligands
- ATP, MG
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MRNA cleavage and polyadenylation factor CLP1 | protein | 428 | 30% helix, 30% strand | Q08685 |
| B | MRNA cleavage and polyadenylation factor CLP1 | protein | 430 | 29% helix, 30% strand | Q08685 |
| C | PCF11P | protein | 27 | 33% helix, 4% strand | N1P6M1 |
| D | PCF11P | protein | 36 | 25% helix, 6% strand | N1P6M1 |
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
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.84 | 0.93 | 51 | ATP, MG |
| 2 | 409 | 0.83 | 0.91 | 53 | ATP, MG |
| 3 | 622 | 0.76 | 0.82 | 55 | empty |
| 4 | 151 | 0.53 | 0.80 | 20 | empty |
| 5 | 158 | 0.53 | 0.80 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–D · 2189 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 1611 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1003 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4C0B · Structure of wild-type Clp1p-Pcf11p (454 -563) complex · the same entry in another collection · chain A against A, 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 0.99
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 N1P6M1
- Elsewhere: RCSB PDB 4C0B · PDBe 4C0B · UniProt Q08685 · UniProt N1P6M1
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