Research workbench
The structure of the teipp associated altered peptide ligand TRH4- P5NLE in complex with H-2D(B)
Analyse The structure of the teipp associated altered peptide ligand TRH4- P5NLE in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E8P
- Type
- protein
- Length
- 759 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; Beta-2-microglobulin; Ceramide…
- EC
- 2.3.1.24
- UniProt
- P01899, P01887, Q9D6K9
- Ligands
- SO4
- Pockets
- 13 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 272 | 25% helix, 39% strand | P01899 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| C, F | Ceramide synthase 5 (EC 2.3.1.24) | protein | 9 | 0% helix, 0% strand | Q9D6K9 |
| D | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 271 | 26% helix, 39% strand | P01899 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 489 | 0.62 | 0.76 | 45 | empty |
| 2 | 441 | 0.59 | 0.75 | 46 | empty |
| 3 | 121 | 0.44 | 0.77 | 23 | empty |
| 4 | 64 | 0.39 | 0.80 | 17 | empty |
| 5 | 75 | 0.39 | 0.78 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1377 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1368 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 952 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 942 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 721 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 5E8P · The structure of the TEIPP associated altered peptide ligand Trh4-p5NLE 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 0.45
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 P01887
- Every structure of UniProt Q9D6K9
- Elsewhere: RCSB PDB 5E8P · PDBe 5E8P · UniProt P01899 · UniProt P01887 · UniProt Q9D6K9
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