Research workbench
The structure of the teipp associated altered peptide ligand TRH4- P2ABU in complex with H-2D(B)
Analyse The structure of the teipp associated altered peptide ligand TRH4- P2ABU in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E8O
- Type
- protein
- Length
- 762 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, D-B alpha chain; Ceramide synthase 5…
- EC
- 2.3.1.24
- UniProt
- P01899, Q9D6K9, P01887
- Pockets
- 10 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 272 | 24% helix, 40% strand | P01899 |
| C, F | Ceramide synthase 5 (EC 2.3.1.24) | protein | 9 | 0% helix, 0% strand | Q9D6K9 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| D | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 274 | 27% helix, 40% strand | P01899 |
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.67 | 0.75 | 65 | empty |
| 2 | 625 | 0.63 | 0.74 | 70 | empty |
| 3 | 95 | 0.44 | 0.79 | 23 | empty |
| 4 | 101 | 0.41 | 0.77 | 22 | empty |
| 5 | 62 | 0.39 | 0.80 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1339 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1279 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 945 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 901 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 738 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 5E8O · The structure of the TEIPP associated altered peptide ligand Trh4-p2ABU in complex with… · the same entry in another collection · chain F against F, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q9D6K9 · AlphaFold monomer V2.0 prediction for ceramide synthase 5 (Q9D6K9) · a predicted model of the same protein · chain C against A, TM-score 0.44
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 P01899
- Every structure of UniProt Q9D6K9
- Every structure of UniProt P01887
- Elsewhere: RCSB PDB 5E8O · PDBe 5E8O · UniProt P01899 · UniProt Q9D6K9 · UniProt P01887
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