Research workbench
The structure of the teipp associated TRH4 peptide in complex with H- 2D(B)
Analyse The structure of the teipp associated TRH4 peptide in complex with H- 2D(B) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E8N
- Type
- protein
- Length
- 1,503 residues
- Chains
- 12
- 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
- 20 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 22% 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, 40% strand | P01899 |
| B, E, H, K | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| C, F, I, L | 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 | 272 | 24% helix, 40% strand | P01899 |
| G | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 269 | 24% helix, 40% strand | P01899 |
| J | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 258 | 25% helix, 37% strand | P01899 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.71 | 0.75 | 81 | empty |
| 2 | 834 | 0.69 | 0.75 | 69 | empty |
| 3 | 670 | 0.67 | 0.76 | 60 | empty |
| 4 | 731 | 0.65 | 0.74 | 73 | empty |
| 5 | 361 | 0.60 | 0.77 | 44 | empty |
Interfaces
15 interfaces between chains.
- J–K · 1330 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1289 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1272 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 1271 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 950 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5E8N · The structure of the TEIPP associated Trh4 peptide in complex with H-2D(b) · the same entry in another collection · chain L against L, 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 P01899
- Every structure of UniProt P01887
- Every structure of UniProt Q9D6K9
- Elsewhere: RCSB PDB 5E8N · PDBe 5E8N · UniProt P01899 · UniProt P01887 · UniProt Q9D6K9
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