MolNFT v1 · #139144 · protein
Crystal structure of seprs-sepcyse from methanocaldococcus jannaschii
5X6C · O-phosphoserine--TRNA(CYS) ligase: “Crystal structure of seprs-sepcyse from methanocaldococcus jannaschii”. X-ray diffraction, 2 ligands (ATP, SO4), 7 pockets (best druggability 0.73). MolNFT v1 #139144 on GenesisL1: 3D structure…
- PDB
- 5X6C
- Type
- protein
- Length
- 1,130 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-phosphoserine--TRNA(CYS) ligase; Uncharacterized protein MJ1481
- EC
- 6.1.1.27
- UniProt
- Q58876
- Ligands
- ATP, SO4
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | O-phosphoserine--TRNA(CYS) ligase (EC 6.1.1.27) | protein | 539 | 40% helix, 25% strand | — |
| E, F | Uncharacterized protein MJ1481 | protein | 26 | 92% helix, 0% strand | Q58876 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate 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 | 265 | 0.73 | 0.87 | 38 | ATP, SO4 |
| 2 | 240 | 0.70 | 0.86 | 34 | ATP, SO4 |
| 3 | 527 | 0.66 | 0.78 | 57 | empty |
| 4 | 165 | 0.47 | 0.76 | 28 | empty |
| 5 | 50 | 0.44 | 0.84 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 687 Ų buried · 21 hydrogen bonds · protein-protein
- A–F · 675 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 665 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 535 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 532 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5X6C · Crystal structure of SepRS-SepCysE from Methanocaldococcus jannaschii · the same entry in another collection · chain A against A, TM-score 1.00
- Q58876 · AlphaFold monomer V2.0 prediction for uncharacterized protein MJ1481 (Q58876) · a predicted model of the same protein · chain E against A, TM-score 0.79
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 Q58876
- Elsewhere: RCSB PDB 5X6C · PDBe 5X6C · UniProt Q58876
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