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Crystal structure of methanoperedens nitroreducens elongation factor 2 bound to gmppcp and magnesium
Analyse Crystal structure of methanoperedens nitroreducens elongation factor 2 bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U45
- Type
- protein
- Length
- 1,429 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor 2
- UniProt
- A0A062V290
- Ligands
- GCP, MG, CL
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Elongation factor 2 | protein | 726 | 38% helix, 27% strand | A0A062V290 |
| B | Elongation factor 2 | protein | 703 | 37% helix, 29% 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
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.77 | 0.79 | 61 | empty |
| 2 | 802 | 0.75 | 0.80 | 75 | empty |
| 3 | 375 | 0.75 | 0.85 | 45 | empty |
| 4 | 373 | 0.73 | 0.84 | 46 | empty |
| 5 | 464 | 0.69 | 0.80 | 75 | empty |
Interfaces
1 interface between chains.
- A–B · 550 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6U45 · Crystal structure of Methanoperedens nitroreducens elongation factor 2 bound to GMPPCP… · 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 6U45 · PDBe 6U45 · UniProt A0A062V290
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