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Crystal structure of methanoperedens nitroreducens elongation factor 2 H595N bound to gmppcp and magnesium (monoclinic crystal form)
Analyse Crystal structure of methanoperedens nitroreducens elongation factor 2 H595N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U44
- Type
- protein
- Length
- 1,430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor 2
- UniProt
- A0A062V290
- Ligands
- GCP, MG, SO4, CL
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Elongation factor 2 | protein | 715 | 38% helix, 28% strand | A0A062V290 |
Ligands and binding sites
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.79 | 0.85 | 76 | empty |
| 2 | 606 | 0.77 | 0.83 | 56 | empty |
| 3 | 1180 | 0.75 | 0.78 | 95 | SO4 |
| 4 | 831 | 0.73 | 0.78 | 79 | empty |
| 5 | 479 | 0.71 | 0.81 | 63 | empty |
Interfaces
1 interface between chains.
- A–B · 866 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6U44 · Crystal structure of Methanoperedens nitroreducens elongation factor 2 H595N bound to… · 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 A0A062V290
- Elsewhere: RCSB PDB 6U44 · PDBe 6U44 · UniProt A0A062V290
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