MolNFT v1 · #94279 · protein
Crystal structure of H-2KB with a disulfide stabilized F pocket in complex with the lcmv derived peptide GP34
4HS3 · H-2 class I histocompatibility antigen, K-B alpha chain: “Crystal structure of H-2KB with a disulfide stabilized F pocket in complex with the lcmv derived peptide GP34”. X-ray diffraction, 1 ligand (PO4), 5 pockets (best…
- PDB
- 4HS3
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, K-B alpha chain; Beta-2-microglobulin; Envelope…
- UniProt
- P01901, P01887, Q9WKU1
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.61
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-B alpha chain | protein | 276 | 27% helix, 38% strand | P01901 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 53% strand | P01887 |
| C | Envelope glycoprotein | protein | 8 | 0% helix, 0% strand | Q9WKU1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.61 | 0.79 | 37 | PO4, MPD |
| 2 | 218 | 0.54 | 0.77 | 19 | empty |
| 3 | 104 | 0.48 | 0.80 | 25 | empty |
| 4 | 122 | 0.45 | 0.78 | 21 | empty |
| 5 | 77 | 0.31 | 0.74 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1357 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 837 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4HS3 · Crystal structure of H-2Kb with a disulfide stabilized F pocket in complex with the LCMV… · 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 0.97
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 P01901
- Every structure of UniProt P01887
- Every structure of UniProt Q9WKU1
- Elsewhere: RCSB PDB 4HS3 · PDBe 4HS3 · UniProt P01901 · UniProt P01887 · UniProt Q9WKU1
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