MolNFT v1 · #191324 · protein
The complex of pre-mRNA-processing factor 19 (PRPF19) peptide kylqvashv presented by H2-kd
8D5K · H-2 class I histocompatibility antigen, K-D alpha chain: “The complex of pre-mRNA-processing factor 19 (PRPF19) peptide kylqvashv presented by H2-kd”. X-ray diffraction, 3 pockets (best druggability 0.68). MolNFT v1 #191324 on…
- PDB
- 8D5K
- Type
- protein
- Length
- 382 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, K-D alpha chain; Beta-2-microglobulin…
- EC
- 2.3.2.27
- UniProt
- P01902, P01887, Q99KP6
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, K-D alpha chain | protein | 273 | 27% helix, 40% strand | P01902 |
| 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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 596 | 0.68 | 0.77 | 51 | empty |
| 2 | 188 | 0.50 | 0.77 | 28 | empty |
| 3 | 60 | 0.38 | 0.79 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1398 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 968 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 8D5K · The complex of Pre-mRNA-Processing Factor 19 (Prpf19) peptide KYLQVASHV Presented by H2-Kd · 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
- P01902 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, K-D alpha… · a predicted model of the same protein · chain A 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 0.43
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 P01902
- Every structure of UniProt P01887
- Every structure of UniProt Q99KP6
- Elsewhere: RCSB PDB 8D5K · PDBe 8D5K · UniProt P01902 · UniProt P01887 · UniProt Q99KP6
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