Research workbench
The structure of a piwi protein from archaeoglobus fulgidus complexed with a 16NT DNA duplex.
Analyse The structure of a piwi protein from archaeoglobus fulgidus complexed with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W42
- Type
- protein + DNA
- Length
- 806 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein; 5'-D(*TP*TP*CP*GP*AP*CP*GP*CP)-3'…
- UniProt
- O28951
- Ligands
- MN
- Pockets
- 9 · best druggability 0.56
Structure
x-ray diffraction · 5 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein | protein | 395 | 38% helix, 26% strand | O28951 |
| B | Putative uncharacterized protein | protein | 389 | 37% helix, 26% strand | O28951 |
| P, R | 5'-D(*TP*TP*CP*GP*AP*CP*GP*CP)-3' | dna | 6 | — | — |
| Q | 5'-D(*GP*TP*CP*GP*AP*AP*TP*TP)-3' | dna | 6 | — | — |
| S | 5'-D(*GP*TP*CP*GP*AP*AP*TP*TP)-3' | dna | 4 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, P, B, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.56 | 0.80 | 29 | empty |
| 2 | 181 | 0.56 | 0.81 | 29 | empty |
| 3 | 218 | 0.48 | 0.75 | 24 | empty |
| 4 | 88 | 0.47 | 0.81 | 20 | empty |
| 5 | 63 | 0.43 | 0.81 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–P · 703 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–R · 697 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–Q · 399 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–S · 349 Ų buried · 3 hydrogen bonds · protein-nucleic
- P–Q · 224 Ų buried · 20 hydrogen bonds · nucleic-nucleic
Compared structures
- 2W42 · The structure of a piwi protein from archaeoglobus fulgidus complexed with a 16NT DNA… · the same entry in another collection · chain S against S, TM-score 1.00
- O28951 · AlphaFold monomer V2.0 prediction for piwi protein AF_1318 (O28951) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 O28951
- Elsewhere: RCSB PDB 2W42 · PDBe 2W42 · UniProt O28951
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