MolNFT v1 · #12155 · protein
Crystal structure of the non-classical MHC class ib qa-2 complexed with a self peptide
1K8D · Qa-2 antigen: “Crystal structure of the non-classical MHC class ib qa-2 complexed with a self peptide”. X-ray diffraction, 4 pockets (best druggability 0.68). MolNFT v1 #12155 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1K8D
- Type
- protein
- Length
- 382 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Qa-2 antigen; Beta-2-microglobulin; 60S ribosomal protein
- UniProt
- P14429, P01887, P14118
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Qa-2 antigen | protein | 274 | 26% helix, 39% strand | P14429 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| P | 60S ribosomal protein | protein | 9 | 0% helix, 0% strand | P14118 |
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 | 635 | 0.68 | 0.77 | 57 | empty |
| 2 | 68 | 0.37 | 0.78 | 23 | empty |
| 3 | 64 | 0.34 | 0.76 | 16 | empty |
| 4 | 72 | 0.28 | 0.72 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1232 Ų buried · 25 hydrogen bonds · protein-protein
- A–P · 907 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1K8D · crystal structure of the non-classical MHC class Ib Qa-2 complexed with a self peptide · the same entry in another collection · chain P against P, 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 0.99
- P14429 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, Q7 alpha… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P14429
- Every structure of UniProt P01887
- Every structure of UniProt P14118
- Elsewhere: RCSB PDB 1K8D · PDBe 1K8D · UniProt P14429 · UniProt P01887 · UniProt P14118
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