MolNFT v1 · #78958 · protein
Crystal structure of cysteinyl-tRNA synthetase (cyss) from borrelia burgdorferi
3SP1: “Crystal structure of cysteinyl-tRNA synthetase (cyss) from borrelia burgdorferi”. X-ray diffraction, 3 ligands (AMP, ZN, CL), 7 pockets (best druggability 0.63). MolNFT v1 #78958 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3SP1
- Type
- protein
- Length
- 857 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteinyl-tRNA synthetase
- EC
- 6.1.1.16
- UniProt
- O51545
- Ligands
- AMP, ZN, CL
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteinyl-tRNA synthetase (EC 6.1.1.16) | protein | 418 | 51% helix, 15% strand | O51545 |
| B | Cysteinyl-tRNA synthetase (EC 6.1.1.16) | protein | 439 | 49% helix, 15% strand | O51545 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains 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 | 316 | 0.63 | 0.79 | 49 | AMP |
| 2 | 324 | 0.61 | 0.78 | 48 | AMP |
| 3 | 64 | 0.53 | 0.87 | 21 | empty |
| 4 | 76 | 0.38 | 0.78 | 17 | empty |
| 5 | 74 | 0.36 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 485 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3SP1 · Crystal structure of cysteinyl-tRNA synthetase (cysS) from Borrelia burgdorferi · the same entry in another collection · chain A against A, TM-score 1.00
- O51545 · AlphaFold monomer V2.0 prediction for cysteine--tRNA ligase (O51545) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 O51545
- Elsewhere: RCSB PDB 3SP1 · PDBe 3SP1 · UniProt O51545
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