Research workbench
Structure of slyd from thermus thermophilus in complex with S2 peptide
Analyse Structure of slyd from thermus thermophilus in complex with S2 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ODL
- Type
- protein
- Length
- 354 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase slyd; 30S ribosomal protein S2
- EC
- 5.2.1.8
- UniProt
- Q5SLE7, P0A7V0
- Ligands
- NH2, CL
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptidyl-prolyl cis-trans isomerase slyd (EC 5.2.1.8) | protein | 150 | 15% helix, 43% strand | Q5SLE7 |
| C | 30S ribosomal protein S2 | protein | 9 | 0% helix, 22% strand | P0A7V0 |
| D, E, F | 30S ribosomal protein S2 | protein | 15 | 0% helix, 20% strand | P0A7V0 |
Ligands and binding sites
- NH2 · Amino group · ion · 4 copies · chains B, C, A, D, E, F
- CL · Chloride ion · ion · 2 copies · chains A, F, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.59 | 0.83 | 23 | empty |
| 2 | 190 | 0.46 | 0.74 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–D · 828 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 790 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 776 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 460 Ų buried · 3 hydrogen bonds · protein-protein
- D–F · 19 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4ODL · Structure of SlyD from Thermus thermophilus in complex with S2 peptide · the same entry in another collection · chain A against A, TM-score 1.00
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 Q5SLE7
- Every structure of UniProt P0A7V0
- Elsewhere: RCSB PDB 4ODL · PDBe 4ODL · UniProt Q5SLE7 · UniProt P0A7V0
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