Research workbench
Structure of slyd from thermus thermophilus in complex with T1 peptide
Analyse Structure of slyd from thermus thermophilus in complex with T1 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ODK
- Type
- protein
- Length
- 164 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase slyd; Guanyl-specific ribonuclease T1
- EC
- 5.2.1.8
- UniProt
- Q5SLE7, P00651
- Ligands
- NH2, CL
- Pockets
- 1 · best druggability 0.29
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-prolyl cis-trans isomerase slyd (EC 5.2.1.8) | protein | 153 | 14% helix, 45% strand | Q5SLE7 |
| B | Guanyl-specific ribonuclease T1 | protein | 8 | 0% helix, 13% strand | P00651 |
| C | Guanyl-specific ribonuclease T1 | protein | 3 | 0% helix, 0% strand | P00651 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.29 | 0.75 | 17 | CL |
Interfaces
2 interfaces between chains.
- A–B · 457 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 369 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4ODK · Structure of SlyD from Thermus thermophilus in complex with T1 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 P00651
- Elsewhere: RCSB PDB 4ODK · PDBe 4ODK · UniProt Q5SLE7 · UniProt P00651
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