Research workbench
Crystal structure of the sepcyss-sepcyse complex from methanocaldococcus jannaschii
Analyse Crystal structure of the sepcyss-sepcyse complex from methanocaldococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WKR
- Type
- protein
- Length
- 1,727 residues
- Chains
- 8
- 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
- 20 · best druggability 0.82
Structure
x-ray diffraction · 7 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-phospho-L-seryl-TRNA:CYS-tRNA synthase (EC 2.5.1.73) | protein | 362 | 38% helix, 18% strand | Q59072 |
| B | O-phospho-L-seryl-TRNA:CYS-tRNA synthase (EC 2.5.1.73) | protein | 364 | 38% helix, 17% strand | Q59072 |
| C | Uncharacterized protein MJ1481 | protein | 68 | 68% helix, 4% strand | Q58876 |
| D, H | Uncharacterized protein MJ1481 | protein | 68 | 60% helix, 4% strand | Q58876 |
| E | O-phospho-L-seryl-TRNA:CYS-tRNA synthase (EC 2.5.1.73) | protein | 365 | 38% helix, 17% strand | Q59072 |
| F | O-phospho-L-seryl-TRNA:CYS-tRNA synthase (EC 2.5.1.73) | protein | 363 | 39% helix, 17% strand | Q59072 |
| G | Uncharacterized protein MJ1481 | protein | 69 | 67% helix, 4% strand | Q58876 |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.82 | 0.85 | 75 | empty |
| 2 | 1168 | 0.81 | 0.82 | 82 | empty |
| 3 | 505 | 0.80 | 0.87 | 61 | empty |
| 4 | 939 | 0.79 | 0.81 | 102 | empty |
| 5 | 115 | 0.77 | 0.97 | 30 | empty |
Interfaces
16 interfaces between chains.
- A–B · 3656 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 3607 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1793 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 1775 Ų buried · 10 hydrogen bonds · protein-protein
- F–H · 843 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 3WKR · Crystal structure of the SepCysS-SepCysE complex from Methanocaldococcus jannaschii · the same entry in another collection · chain H against H, 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 B 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 3WKR · PDBe 3WKR · UniProt Q59072 · UniProt Q58876
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