MolNFT v1 · #33398 · protein
Crystal structure of methanosarcina barkeri seryl-tRNA synthetase complexed with ATP
2CJA: “Crystal structure of methanosarcina barkeri seryl-tRNA synthetase complexed with ATP”. X-ray diffraction, 4 ligands (ATP, ZN, MG), 7 pockets (best druggability 0.67). MolNFT v1 #33398 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2CJA
- Type
- protein
- Length
- 966 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Seryl-tRNA synthetase
- EC
- 6.1.1.11
- UniProt
- Q46AN5
- Ligands
- ATP, ZN, MG, CL
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Seryl-tRNA synthetase (EC 6.1.1.11) | protein | 477 | 37% helix, 25% strand | Q46AN5 |
| B | Seryl-tRNA synthetase (EC 6.1.1.11) | protein | 489 | 35% helix, 26% strand | Q46AN5 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains 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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.67 | 0.78 | 53 | empty |
| 2 | 288 | 0.61 | 0.80 | 32 | ZN, MG, ATP |
| 3 | 371 | 0.61 | 0.77 | 38 | ZN, ATP |
| 4 | 116 | 0.38 | 0.74 | 19 | empty |
| 5 | 69 | 0.33 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 5202 Ų buried · 69 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified (engineered).
Compared structures
- 2CJA · Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase complexed with ATP · the same entry in another collection · chain A against A, TM-score 1.00
- Q46AN5 · AlphaFold monomer V2.0 prediction for type-2 serine--tRNA ligase (Q46AN5) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q46AN5
- Elsewhere: RCSB PDB 2CJA · PDBe 2CJA · UniProt Q46AN5
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