MolNFT v1 · #59804 · protein
The 1.6 a crystal structure of mshc: the rate limiting enzyme in the mycothiol biosynthetic pathway
3C8Z · Cysteinyl-tRNA synthetase: “The 1.6 a crystal structure of mshc: the rate limiting enzyme in the mycothiol biosynthetic pathway”. X-ray diffraction, 3 ligands (5CA, ZN, SO4), 6 pockets (best druggability 0.77). MolNFT v1 #59804 on…
- PDB
- 3C8Z
- Type
- protein
- Length
- 800 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
- A0QZY0
- Ligands
- 5CA, ZN, SO4
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteinyl-tRNA synthetase (EC 6.1.1.16) | protein | 399 | 45% helix, 16% strand | A0QZY0 |
| B | Cysteinyl-tRNA synthetase (EC 6.1.1.16) | protein | 401 | 45% helix, 14% strand | A0QZY0 |
Ligands and binding sites
- 5CA · 5'-O-(N-(L-cysteinyl)-sulfamoyl)adenosine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.77 | 0.83 | 70 | empty |
| 2 | 463 | 0.70 | 0.81 | 49 | 5CA, ZN |
| 3 | 400 | 0.68 | 0.81 | 45 | 5CA, ZN |
| 4 | 55 | 0.58 | 0.90 | 18 | SO4 |
| 5 | 54 | 0.43 | 0.83 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 811 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3C8Z · The 1.6 A Crystal Structure of MshC: The Rate Limiting Enzyme in the Mycothiol… · the same entry in another collection · chain B against B, TM-score 1.00
- A0QZY0 · AlphaFold monomer V2.0 prediction for L-CYSTEINE:1D-myo-inositol… · 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 A0QZY0
- Elsewhere: RCSB PDB 3C8Z · PDBe 3C8Z · UniProt A0QZY0
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