Research workbench
Crystal structure of transcription factor iib mja mini-intein
Analyse Crystal structure of transcription factor iib mja mini-intein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O9J
- Type
- protein
- Length
- 365 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription initiation factor IIB,TRANSCRIPTION initiation factor iib
- EC
- 3.1.-.-
- UniProt
- Q58192
- Ligands
- NH4
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription initiation factor IIB,TRANSCRIPTION initiation factor iib (EC 3.1.-.-) | protein | 182 | 9% helix, 56% strand | Q58192 |
| B | Transcription initiation factor IIB,TRANSCRIPTION initiation factor iib (EC 3.1.-.-) | protein | 183 | 7% helix, 53% strand | Q58192 |
Ligands and binding sites
- NH4 · Ammonium ion · ion · 10 copies · chains A, B
- GOL · Glycerol · additive · 14 copies · chains A, B
- DIO · 1,4-diethylene dioxide · additive · 6 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.60 | 0.81 | 28 | empty |
| 2 | 64 | 0.34 | 0.76 | 17 | DIO, NH4 |
Interfaces
1 interface between chains.
- A–B · 506 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5O9J · Crystal structure of transcription factor IIB Mja mini-intein · the same entry in another collection · chain A against A, TM-score 1.00
- Q58192 · AlphaFold monomer V2.0 prediction for transcription initiation factor iib (Q58192) · a predicted model of the same protein · chain B against A, TM-score 0.76
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 Q58192
- Elsewhere: RCSB PDB 5O9J · PDBe 5O9J · UniProt Q58192
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