Research workbench
Crystal structure of a SARS corona virus derived peptide bound to the human major histocompatibility complex class I molecule HLA-B*1501
Analyse Crystal structure of a SARS corona virus derived peptide bound to the human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C9N
- Type
- protein
- Length
- 384 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-15 alpha chain; Beta-2-microglobulin; Peptide…
- UniProt
- P30464, P61769
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-15 alpha chain | protein | 276 | 28% helix, 39% strand | P30464 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Peptide antigen | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- PG4 · Tetraethylene glycol · additive · chains A, C
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 59 | EPE |
| 2 | 124 | 0.45 | 0.78 | 23 | empty |
| 3 | 88 | 0.42 | 0.79 | 17 | empty |
| 4 | 50 | 0.38 | 0.81 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1365 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 915 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3C9N · Crystal Structure of a SARS Corona Virus Derived Peptide Bound to the Human Major… · the same entry in another collection · chain A against A, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B 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 P30464
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 3C9N · PDBe 3C9N · UniProt P30464 · UniProt P61769
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.