Research workbench
Yeast POLY(A) polymerase in complex with FIP1 residues 80-105
Analyse Yeast POLY(A) polymerase in complex with FIP1 residues 80-105 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C66
- Type
- protein
- Length
- 1,105 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POLY(A) polymerase; Pre-mRNA polyadenylation factor FIP1
- EC
- 2.7.7.19
- UniProt
- P29468, P45976
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POLY(A) polymerase (EC 2.7.7.19) | protein | 529 | 44% helix, 17% strand | P29468 |
| B | POLY(A) polymerase (EC 2.7.7.19) | protein | 529 | 44% helix, 17% strand | P29468 |
| C | Pre-mRNA polyadenylation factor FIP1 | protein | 24 | 29% helix, 21% strand | P45976 |
| D | Pre-mRNA polyadenylation factor FIP1 | protein | 23 | 13% helix, 22% strand | P45976 |
Ligands and binding sites
- GOL · Glycerol · additive · 11 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.70 | 0.76 | 73 | GOL |
| 2 | 453 | 0.60 | 0.75 | 55 | GOL |
| 3 | 261 | 0.56 | 0.77 | 40 | MES, GOL |
| 4 | 91 | 0.46 | 0.81 | 18 | empty |
| 5 | 95 | 0.41 | 0.77 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–D · 983 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 912 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 566 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3C66 · Yeast poly(A) polymerase in complex with Fip1 residues 80-105 · the same entry in another collection · chain D against D, TM-score 1.00
- P29468 · AlphaFold monomer V2.0 prediction for POLY(A) polymerase (P29468) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P45976 · AlphaFold monomer V2.0 prediction for pre-mRNA polyadenylation factor FIP1 (P45976) · a predicted model of the same protein · chain C against A, TM-score 0.25
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 P29468
- Every structure of UniProt P45976
- Elsewhere: RCSB PDB 3C66 · PDBe 3C66 · UniProt P29468 · UniProt P45976
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