MolNFT v1 · #102316 · protein
Protein complex of CLP1 bound to ATP and MG2+ with PCF11DELTAN454DELTAC563 of S. cerevisiae
4OI4 · MRNA cleavage and polyadenylation factor CLP1: “Protein complex of CLP1 bound to ATP and MG2+ with PCF11DELTAN454DELTAC563 of S. cerevisiae”. X-ray diffraction, 2 ligands (ATP, MG), 9 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 4OI4
- Type
- protein
- Length
- 912 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA cleavage and polyadenylation factor CLP1; Protein PCF11
- EC
- 2.7.1.78
- UniProt
- Q08685, P39081
- Ligands
- ATP, MG
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MRNA cleavage and polyadenylation factor CLP1 (EC 2.7.1.78) | protein | 428 | 29% helix, 31% strand | Q08685 |
| C | MRNA cleavage and polyadenylation factor CLP1 (EC 2.7.1.78) | protein | 427 | 30% helix, 31% strand | Q08685 |
| B | Protein PCF11 | protein | 25 | 36% helix, 4% strand | P39081 |
| D | Protein PCF11 | protein | 24 | 38% helix, 4% strand | P39081 |
| U | Protein PCF11 | protein | 8 | 0% helix, 0% strand | P39081 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
- GOL · Glycerol · additive · 3 copies · chains A, C
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 | 385 | 0.83 | 0.92 | 51 | ATP, MG, GOL |
| 2 | 385 | 0.82 | 0.91 | 48 | ATP, MG, GOL |
| 3 | 813 | 0.77 | 0.81 | 70 | empty |
| 4 | 180 | 0.55 | 0.80 | 21 | GOL |
| 5 | 148 | 0.55 | 0.81 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1656 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1632 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 940 Ų buried · 20 hydrogen bonds · protein-protein
- A–U · 140 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4OI4 · Protein complex of Clp1 bound to ATP and Mg2+ with Pcf11deltaN454deltaC563 of S.… · the same entry in another collection · chain U against U, 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 C against A, TM-score 0.98
- P39081 · AlphaFold monomer V2.0 prediction for protein PCF11 (P39081) · a predicted model of the same protein · chain B against A, TM-score 0.50
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 4OI4 · PDBe 4OI4 · UniProt Q08685 · UniProt P39081
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.