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Spore photoproduct lyase C140A/S76C mutant with bound AdoMet and dinucleoside spore photoproduct
Analyse Spore photoproduct lyase C140A/S76C mutant with bound AdoMet and dinucleoside… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RH1
- Type
- protein
- Length
- 340 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Geobacillus thermodenitrificans NG80-2
- Molecule
- Spore photoproduct lyase
- EC
- 4.1.99.14
- UniProt
- A4IQU1
- Ligands
- SF4, EEM, 0TT, SO4
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.6 · 1 distinct chain · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spore photoproduct lyase (EC 4.1.99.14) | protein | 340 | 38% helix, 21% strand | A4IQU1 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- 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 · chains A
- 0TT · 1-[(2R,4S,5R)-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-5-[[(5R)-1-[(2R,4S,5R)-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-5-methyl-2,4-bis(oxidanylidene)-1,3-diazinan-5-yl]methyl]pyrimidine-2,4-dione · ligand · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 639 | 0.78 | 0.83 | 63 | SF4, EEM, SO4, 0TT |
| 2 | 104 | 0.38 | 0.75 | 17 | empty |
| 3 | 74 | 0.34 | 0.76 | 13 | empty |
Compared structures
- 4RH1 · Spore photoproduct lyase C140A/S76C mutant with bound adomet and dinucleoside spore… · the same entry in another collection · chain A against A, TM-score 1.00
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 A4IQU1
- Elsewhere: RCSB PDB 4RH1 · PDBe 4RH1 · UniProt A4IQU1
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