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Crystal structure of sepcyse-sepcyss in complex with trnacys from methanocaldococcus jannaschii
Analyse Crystal structure of sepcyse-sepcyss in complex with trnacys from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X6B
- Type
- protein + RNA
- Length
- 1,064 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-phospho-L-seryl-TRNA:CYS-tRNA synthase; Uncharacterized protein MJ1481; Trnacys
- UniProt
- Q58876
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | O-phospho-L-seryl-TRNA:CYS-tRNA synthase | protein | 367 | 41% helix, 17% strand | — |
| J | O-phospho-L-seryl-TRNA:CYS-tRNA synthase | protein | 377 | 40% helix, 16% strand | — |
| E | Uncharacterized protein MJ1481 | protein | 68 | 68% helix, 6% strand | Q58876 |
| F | Uncharacterized protein MJ1481 | protein | 177 | 51% helix, 10% strand | Q58876 |
| P | Trnacys | rna | 75 | — | — |
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1144 | 0.85 | 0.86 | 101 | empty |
| 2 | 624 | 0.81 | 0.86 | 51 | empty |
| 3 | 865 | 0.75 | 0.78 | 94 | empty |
| 4 | 73 | 0.74 | 0.98 | 23 | empty |
| 5 | 285 | 0.63 | 0.81 | 27 | empty |
Interfaces
9 interfaces between chains.
- I–J · 4021 Ų buried · 57 hydrogen bonds · protein-protein
- E–F · 1852 Ų buried · 13 hydrogen bonds · protein-protein
- I–P · 1116 Ų buried · 28 hydrogen bonds · protein-nucleic
- F–P · 1038 Ų buried · 20 hydrogen bonds · protein-nucleic
- J–F · 845 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 5X6B · Crystal structure of SepCysE-SepCysS in complex with tRNACys from Methanocaldococcus… · the same entry in another collection · chain J against J, 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 0.98
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 Q58876
- Elsewhere: RCSB PDB 5X6B · PDBe 5X6B · UniProt Q58876
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