MolNFT v1 · #35308 · protein
Crystal structure of sep-TRNA:CYS-tRNA synthase from archaeoglobus fulgidus
2E7I: “Crystal structure of sep-TRNA:CYS-tRNA synthase from archaeoglobus fulgidus”. X-ray diffraction, 2 ligands (PLP, SO4), 7 pockets (best druggability 0.55). MolNFT v1 #35308 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2E7I
- Type
- protein
- Length
- 688 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sep-TRNA:CYS-tRNA synthase
- UniProt
- O30207
- Ligands
- PLP, SO4
- Pockets
- 7 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Sep-TRNA:CYS-tRNA synthase | protein | 344 | 45% helix, 16% strand | O30207 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 290 | 0.55 | 0.76 | 41 | SO4 |
| 2 | 138 | 0.54 | 0.81 | 20 | empty |
| 3 | 249 | 0.51 | 0.75 | 39 | SO4 |
| 4 | 121 | 0.50 | 0.80 | 15 | empty |
| 5 | 66 | 0.45 | 0.83 | 28 | PLP |
Interfaces
1 interface between chains.
- A–B · 708 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2E7I · Crystal Structure of Sep-tRNA:Cys-tRNA Synthase from Archaeoglobus fulgidus · the same entry in another collection · chain A against A, TM-score 1.00
- O30207 · AlphaFold monomer V2.0 prediction for O-phospho-L-seryl-TRNA:CYS-tRNA synthase 1 (O30207) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O30207
- Elsewhere: RCSB PDB 2E7I · PDBe 2E7I · UniProt O30207
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