Research workbench
Functional implications from the CID1 POLY(U) polymerase crystal structure
Analyse Functional implications from the CID1 POLY(U) polymerase crystal structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EP7
- Type
- protein
- Length
- 634 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POLY(A) RNA polymerase protein CID1
- EC
- 2.7.7.-
- UniProt
- O13833
- Ligands
- UTP, MG
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POLY(A) RNA polymerase protein CID1 (EC 2.7.7.-) | protein | 319 | 43% helix, 13% strand | O13833 |
| B | POLY(A) RNA polymerase protein CID1 (EC 2.7.7.-) | protein | 315 | 46% helix, 14% strand | O13833 |
Ligands and binding sites
- UTP · Uridine 5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.77 | 0.81 | 69 | MG |
| 2 | 528 | 0.65 | 0.76 | 50 | UTP, MG |
| 3 | 270 | 0.58 | 0.78 | 31 | UTP, MG |
| 4 | 55 | 0.32 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 583 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4EP7 · Functional implications from the Cid1 poly(U) polymerase crystal structure · the same entry in another collection · chain A against A, TM-score 1.00
- O13833 · AlphaFold monomer V2.0 prediction for terminal uridylyltransferase CID1 (O13833) · 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 O13833
- Elsewhere: RCSB PDB 4EP7 · PDBe 4EP7 · UniProt O13833
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