Research workbench
Structure of slyd delta-if from thermus thermophilus in complex with S2-W23A peptide
Analyse Structure of slyd delta-if from thermus thermophilus in complex with S2-W23A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ODP
- Type
- protein
- Length
- 106 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase slyd, peptidyl-prolyl cis-trans isomerase FKBP1A…
- EC
- 5.2.1.8
- UniProt
- Q5SLE7, P62942, P0A7V0
- Ligands
- CA, NI, CL
- Pockets
- 1 · best druggability 0.26
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-prolyl cis-trans isomerase slyd, peptidyl-prolyl cis-trans isomerase FKBP1A chimera (EC 5.2.1.8) | protein | 101 | 16% helix, 45% strand | Q5SLE7, P62942 |
| B | 30S ribosomal protein S2 | protein | 5 | 0% helix, 20% strand | P0A7V0 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A
- NI · Nickel (II) ion · metal · chains A
- CL · Chloride ion · ion · chains A, B
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 | 53 | 0.26 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 352 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4ODP · Structure of SlyD delta-IF from Thermus thermophilus in complex with S2-W23A peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P62942 · AlphaFold monomer V2.0 prediction for peptidyl-prolyl cis-trans isomerase FKBP1A (P62942) · a predicted model of the same protein · chain A against A, TM-score 0.73
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 P62942
- Every structure of UniProt P0A7V0
- Elsewhere: RCSB PDB 4ODP · PDBe 4ODP · UniProt Q5SLE7 · UniProt P62942 · UniProt P0A7V0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.