Research workbench
Structure of CID1 in complex with its short product apu
Analyse Structure of CID1 in complex with its short product apu in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NKU
- Type
- protein + RNA
- Length
- 634 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POLY(A) RNA polymerase protein CID1; 5'-R(*AP*U)-3'
- EC
- 2.7.7.-
- UniProt
- O13833
- Ligands
- MG, BR
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POLY(A) RNA polymerase protein CID1 (EC 2.7.7.-) | protein | 320 | 44% helix, 12% strand | O13833 |
| B | POLY(A) RNA polymerase protein CID1 (EC 2.7.7.-) | protein | 310 | 48% helix, 12% strand | O13833 |
| D, H | 5'-R(*AP*U)-3' | rna | 2 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B
- BR · Bromide ion · ion · 3 copies · chains A, B, H, D
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 | 934 | 0.71 | 0.76 | 67 | MG |
| 2 | 387 | 0.58 | 0.76 | 47 | empty |
| 3 | 266 | 0.54 | 0.76 | 39 | empty |
| 4 | 51 | 0.34 | 0.78 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–D · 370 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–H · 369 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–B · 317 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4NKU · Structure of Cid1 in complex with its short product ApU · the same entry in another collection · chain B against B, 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 4NKU · PDBe 4NKU · UniProt O13833
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