Research workbench
Crystal structure of a putative endoribonuclease L-psp from entamoeba histolytica with higher solvent content and an ordered N-terminal tag
Analyse Crystal structure of a putative endoribonuclease L-psp from entamoeba… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MQW
- Type
- protein
- Length
- 817 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative endoribonuclease L-psp
- UniProt
- C4LXT9
- Ligands
- SO4
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 29% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative endoribonuclease L-psp | protein | 132 | 30% helix, 32% strand | C4LXT9 |
| B | Putative endoribonuclease L-psp | protein | 140 | 29% helix, 31% strand | C4LXT9 |
| C | Putative endoribonuclease L-psp | protein | 136 | 29% helix, 32% strand | C4LXT9 |
| D | Putative endoribonuclease L-psp | protein | 141 | 28% helix, 30% strand | C4LXT9 |
| E | Putative endoribonuclease L-psp | protein | 135 | 29% helix, 32% strand | C4LXT9 |
| F | Putative endoribonuclease L-psp | protein | 133 | 29% helix, 33% strand | C4LXT9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains B, D, C, F, A, E
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D, E, F
- FLC · Citrate anion · additive · 5 copies · chains A, C, B, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.86 | 0.98 | 29 | GOL |
| 2 | 233 | 0.86 | 0.98 | 34 | GOL |
| 3 | 143 | 0.80 | 0.97 | 24 | empty |
| 4 | 121 | 0.66 | 0.89 | 22 | FLC |
| 5 | 120 | 0.65 | 0.88 | 19 | FLC |
Interfaces
12 interfaces between chains.
- C–D · 1275 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 1151 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 926 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 921 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 920 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3MQW · Crystal structure of a putative endoribonuclease L-PSP from Entamoeba histolytica with… · 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 C4LXT9
- Elsewhere: RCSB PDB 3MQW · PDBe 3MQW · UniProt C4LXT9
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