MolNFT v1 · #113776 · protein
Structure of the SAM-dependent RRNA:ACP-transferase TSR3 from vulcanisaeta distributa
5APG: “Structure of the SAM-dependent RRNA:ACP-transferase TSR3 from vulcanisaeta distributa”. X-ray diffraction, 1 ligand (EEM), 7 pockets (best druggability 0.71). MolNFT v1 #113776 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5APG
- Type
- protein
- Length
- 552 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TSR3
- EC
- 2.5.1.-
- UniProt
- E1QU22
- Ligands
- EEM
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | TSR3 (EC 2.5.1.-) | protein | 184 | 44% helix, 13% strand | E1QU22 |
Ligands and binding sites
- EEM · [(3S)-3-amino-4-hydroxy-4-oxo-butyl]-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]-methyl-selanium · ligand · 3 copies · chains A, B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 742 | 0.71 | 0.77 | 66 | empty |
| 2 | 273 | 0.69 | 0.84 | 39 | empty |
| 3 | 260 | 0.69 | 0.84 | 36 | EEM |
| 4 | 275 | 0.69 | 0.84 | 36 | EEM |
| 5 | 291 | 0.68 | 0.83 | 42 | EEM |
Interfaces
3 interfaces between chains.
- A–B · 695 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 536 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 307 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 5APG · Structure of the SAM-dependent rRNA:acp-transferase Tsr3 from Vulcanisaeta distributa · the same entry in another collection · chain B against B, TM-score 1.00
- E1QU22 · AlphaFold monomer V2.0 prediction for 16S rRNA aminocarboxypropyltransferase (E1QU22) · 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 E1QU22
- Elsewhere: RCSB PDB 5APG · PDBe 5APG · UniProt E1QU22
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