MolNFT v1 · #32107 · protein + RNA
The structure of a piwi protein from archaeoglobus fulgidus complexed with a 16NT siRNA duplex.
2BGG · Protein AF1318: “The structure of a piwi protein from archaeoglobus fulgidus complexed with a 16NT siRNA duplex.”. X-ray diffraction, 1 ligand (MN), 10 pockets (best druggability 0.67). MolNFT v1 #32107 on GenesisL1: 3D structure…
- PDB
- 2BGG
- Type
- protein + RNA
- Length
- 818 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein AF1318; 5'-R(*UP*UP*CP*GP*AP*CP*GP*CP)-3'; 5'-R(*GP*UP*CP*GP*AP*AP*UP*UP)-3'
- UniProt
- O28951
- Ligands
- MN
- Pockets
- 10 · best druggability 0.67
Structure
x-ray diffraction · 5 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein AF1318 | protein | 395 | 38% helix, 26% strand | O28951 |
| B | Protein AF1318 | protein | 394 | 38% helix, 26% strand | O28951 |
| P, R | 5'-R(*UP*UP*CP*GP*AP*CP*GP*CP)-3' | rna | 8 | — | — |
| Q | 5'-R(*GP*UP*CP*GP*AP*AP*UP*UP)-3' | rna | 8 | — | — |
| S | 5'-R(*GP*UP*CP*GP*AP*AP*UP*UP)-3' | rna | 5 | — | — |
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
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 584 | 0.67 | 0.77 | 72 | empty |
| 2 | 85 | 0.59 | 0.88 | 22 | empty |
| 3 | 307 | 0.58 | 0.78 | 41 | empty |
| 4 | 152 | 0.50 | 0.79 | 25 | empty |
| 5 | 165 | 0.48 | 0.77 | 25 | empty |
Interfaces
7 interfaces between chains.
- B–R · 683 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–P · 667 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–Q · 525 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–B · 398 Ų buried · 9 hydrogen bonds · protein-protein
- R–S · 292 Ų buried · 31 hydrogen bonds · nucleic-nucleic
Compared structures
- 2BGG · The structure of a Piwi protein from Archaeoglobus fulgidus complexed with a 16nt siRNA… · 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 2BGG · PDBe 2BGG · UniProt O28951
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