MolNFT v2 · #217415 · protein + DNA + RNA
Crystal structure of cA4-bound Can2 (E341A) in complex with oligo-C DNA
8Q43 · DUF1887 family protein: “Crystal structure of cA4-bound Can2 (E341A) in complex with oligo-C DNA”. X-ray diffraction at 2.28, 1 ligand (MN), 11 pockets (best druggability 0.80). MolNFT v2 #217415 on GenesisL1: 3D structure, binding…
- PDB
- 8Q43
- Type
- protein + DNA + RNA
- Length
- 850 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.28
- Source
- Thermoanaerobacter brockii subsp. finnii Ako-1; SYNTHETIC CONSTRUCT
- Molecule
- DUF1887 family protein; DNA (5'-D(*CP*CP*CP*CP*C)-3'); Cyclic tetraadenosine…
- UniProt
- E8URK0
- Ligands
- MN
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.28 · 5 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DUF1887 family protein | protein | 411 | 46% helix, 18% strand | E8URK0 |
| B | DUF1887 family protein | protein | 428 | 48% helix, 19% strand | E8URK0 |
| C | DNA (5'-D(*CP*CP*CP*CP*C)-3') | dna | 3 | — | — |
| D | DNA (5'-D(*CP*CP*CP*CP*C)-3') | dna | 4 | — | — |
| X | Cyclic tetraadenosine monophosphate (cA4) | rna | 4 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 480 | 0.80 | 0.88 | 53 | empty |
| 2 | 1012 | 0.72 | 0.76 | 65 | empty |
| 3 | 159 | 0.58 | 0.83 | 28 | MN |
| 4 | 191 | 0.57 | 0.80 | 33 | empty |
| 5 | 133 | 0.56 | 0.83 | 27 | empty |
Interfaces
7 interfaces between chains.
- A–B · 3156 Ų buried · 53 hydrogen bonds · protein-protein
- B–X · 670 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–X · 661 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–D · 478 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–C · 453 Ų buried · 14 hydrogen bonds · protein-nucleic
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 E8URK0
- Elsewhere: RCSB PDB 8Q43 · PDBe 8Q43 · UniProt E8URK0
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