Research workbench
Crystal structure of the sepcyss-sepcyse N-terminal domain complex from
Analyse Crystal structure of the sepcyss-sepcyse N-terminal domain complex from in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WKS
- Type
- protein
- Length
- 873 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-phospho-L-seryl-TRNA:CYS-tRNA synthase; Uncharacterized protein MJ1481
- EC
- 2.5.1.73
- UniProt
- Q59072, Q58876
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-phospho-L-seryl-TRNA:CYS-tRNA synthase (EC 2.5.1.73) | protein | 364 | 40% helix, 17% strand | Q59072 |
| B | O-phospho-L-seryl-TRNA:CYS-tRNA synthase (EC 2.5.1.73) | protein | 371 | 39% helix, 16% strand | Q59072 |
| C | Uncharacterized protein MJ1481 | protein | 68 | 68% helix, 4% strand | Q58876 |
| D | Uncharacterized protein MJ1481 | protein | 70 | 64% helix, 4% strand | Q58876 |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1044 | 0.78 | 0.80 | 107 | empty |
| 2 | 106 | 0.75 | 0.96 | 28 | empty |
| 3 | 905 | 0.75 | 0.78 | 79 | empty |
| 4 | 76 | 0.44 | 0.81 | 14 | empty |
| 5 | 55 | 0.33 | 0.77 | 13 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3776 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1785 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 860 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 831 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 299 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 disulfide (cofactor, disulfide).
Compared structures
- 3WKS · Crystal structure of the SepCysS-SepCysE N-terminal domain complex from · the same entry in another collection · chain D against D, TM-score 1.00
- Q59072 · AlphaFold monomer V2.0 prediction for O-phospho-L-seryl-TRNA:CYS-tRNA synthase (Q59072) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q58876 · AlphaFold monomer V2.0 prediction for uncharacterized protein MJ1481 (Q58876) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q59072
- Every structure of UniProt Q58876
- Elsewhere: RCSB PDB 3WKS · PDBe 3WKS · UniProt Q59072 · UniProt Q58876
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