MolNFT v1 · #144270 · protein
Crystal structure of rapa, a SWI2/SNF2 protein that recycles RNA polymerase during transcription
6BOG · RNA polymerase-associated protein rapa: “Crystal structure of rapa, a SWI2/SNF2 protein that recycles RNA polymerase during transcription”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.83). MolNFT v1 #144270 on…
- PDB
- 6BOG
- Type
- protein
- Length
- 1,934 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA polymerase-associated protein rapa
- EC
- 3.6.4.-
- UniProt
- B7MAI2
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA polymerase-associated protein rapa (EC 3.6.4.-) | protein | 967 | 45% helix, 17% strand | B7MAI2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 963 | 0.83 | 0.84 | 94 | empty |
| 2 | 707 | 0.82 | 0.86 | 81 | empty |
| 3 | 1089 | 0.82 | 0.83 | 94 | SO4 |
| 4 | 1200 | 0.78 | 0.80 | 84 | SO4 |
| 5 | 362 | 0.72 | 0.84 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 1069 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 46 modified (engineered).
Compared structures
- 6BOG · Crystal structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during… · the same entry in another collection · chain A against A, TM-score 1.00
- B7MAI2 · AlphaFold monomer V2.0 prediction for RNA polymerase-associated protein rapa (B7MAI2) · a predicted model of the same protein · chain A against A, TM-score 0.83
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 B7MAI2
- Elsewhere: RCSB PDB 6BOG · PDBe 6BOG · UniProt B7MAI2
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