Research workbench
The complex of pre-mRNA-processing factor 19 (PRPF19) neoantigen kylqvashv presented by H2-kd
Analyse The complex of pre-mRNA-processing factor 19 (PRPF19) neoantigen kylqvashv… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8D5J
- Type
- protein
- Length
- 384 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I heavy chain maturation peptide H-2K(D); Beta-2-microglobulin…
- EC
- 2.3.2.27
- UniProt
- Q6RJ37, P01887, Q99KP6
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I heavy chain maturation peptide H-2K(D) | protein | 275 | 25% helix, 39% strand | Q6RJ37 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P01887 |
| C | Pre-mRNA-processing factor 19 (EC 2.3.2.27) | protein | 9 | 0% helix, 0% strand | Q99KP6 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.68 | 0.77 | 57 | empty |
| 2 | 163 | 0.49 | 0.77 | 28 | empty |
| 3 | 64 | 0.42 | 0.81 | 24 | empty |
| 4 | 57 | 0.29 | 0.75 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1361 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 984 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 8D5J · The complex of Pre-mRNA-Processing Factor 19 (Prpf19) neoantigen KYLQVASHV Presented by… · the same entry in another collection · chain A against A, 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
- Q99KP6 · AlphaFold monomer V2.0 prediction for pre-mRNA-processing factor 19 (Q99KP6) · 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 Q6RJ37
- Every structure of UniProt P01887
- Every structure of UniProt Q99KP6
- Elsewhere: RCSB PDB 8D5J · PDBe 8D5J · UniProt Q6RJ37 · UniProt P01887 · UniProt Q99KP6
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