Research workbench
An nt-acetylated peptide complexed with HLA-B*3901
Analyse An nt-acetylated peptide complexed with HLA-B*3901 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O2C
- Type
- protein
- Length
- 382 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-39 alpha chain; Beta-2-microglobulin; Peptide…
- UniProt
- P30475, P61769, O00571
- Ligands
- ACE
- Pockets
- 4 · best druggability 0.69
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-39 alpha chain | protein | 274 | 28% helix, 39% strand | P30475 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Peptide from ATP-dependent RNA helicase DDX3X | protein | 9 | 0% helix, 0% strand | O00571 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, C
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 | 607 | 0.69 | 0.78 | 51 | empty |
| 2 | 147 | 0.47 | 0.78 | 28 | empty |
| 3 | 66 | 0.43 | 0.81 | 16 | empty |
| 4 | 95 | 0.42 | 0.78 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1342 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 824 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 4O2C · An Nt-acetylated peptide complexed with HLA-B*3901 · 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 0.99
- O00571 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase DDX3X (O00571) · a predicted model of the same protein · chain C against A, TM-score 0.40
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 P30475
- Every structure of UniProt P61769
- Every structure of UniProt O00571
- Elsewhere: RCSB PDB 4O2C · PDBe 4O2C · UniProt P30475 · UniProt P61769 · UniProt O00571
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