MolNFT v2 · #3547 · protein + RNA
X-ray crystal structure of the POLY(A)-binding protein in complex with polyadenylate RNA
1CVJ · 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3': “X-ray crystal structure of the POLY(A)-binding protein in complex with polyadenylate RNA”. X-ray diffraction at 2.6, 1 ligand (AMP), 20 pockets (best druggability 0.68). MolNFT v2 #3547 on…
- PDB
- 1CVJ
- Type
- protein + RNA
- Length
- 1,304 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'; Polyadenylate binding protein 1
- UniProt
- P11940
- Ligands
- AMP
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · resolution 2.6 · 10 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M | 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3' | rna | 9 | — | — |
| N, O, P, R, S, T | 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3' | rna | 7 | — | — |
| Q | 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3' | rna | 8 | — | — |
| A | Polyadenylate binding protein 1 | protein | 169 | 23% helix, 35% strand | P11940 |
| B | Polyadenylate binding protein 1 | protein | 151 | 28% helix, 31% strand | P11940 |
| C, E | Polyadenylate binding protein 1 | protein | 168 | 27% helix, 34% strand | P11940 |
| D | Polyadenylate binding protein 1 | protein | 161 | 27% helix, 32% strand | P11940 |
| F | Polyadenylate binding protein 1 | protein | 131 | 18% helix, 27% strand | P11940 |
| G | Polyadenylate binding protein 1 | protein | 165 | 28% helix, 32% strand | P11940 |
| H | Polyadenylate binding protein 1 | protein | 132 | 23% helix, 33% strand | P11940 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 8 copies · chains N, B, G, O, C, H, Q, A, E, S, F, M, P, D, R, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.68 | 0.95 | 21 | empty |
| 2 | 63 | 0.67 | 0.95 | 21 | empty |
| 3 | 50 | 0.62 | 0.94 | 21 | empty |
| 4 | 187 | 0.54 | 0.79 | 30 | empty |
| 5 | 188 | 0.54 | 0.79 | 29 | empty |
Interfaces
48 interfaces between chains.
- M–A · 1426 Ų buried · 39 hydrogen bonds · protein-nucleic
- Q–E · 1385 Ų buried · 39 hydrogen bonds · protein-nucleic
- S–G · 1254 Ų buried · 37 hydrogen bonds · protein-nucleic
- O–C · 1251 Ų buried · 33 hydrogen bonds · protein-nucleic
- P–D · 1245 Ų buried · 38 hydrogen bonds · protein-nucleic
Compared structures
- 1CVJ · X-ray crystal structure of the POLY(A)-binding protein in complex with polyadenylate RNA · the same entry in another collection · chain T against T, TM-score 1.00
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 P11940
- Elsewhere: RCSB PDB 1CVJ · PDBe 1CVJ · UniProt P11940
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