Research workbench
A peptide complexed with HLA-B*3901
Analyse A 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
- 4O2F
- Type
- protein
- Length
- 762 residues
- Chains
- 6
- 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
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen, B-39 alpha chain | protein | 274 | 28% helix, 39% strand | P30475 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C, F | Peptide from ATP-dependent RNA helicase DDX3X | protein | 8 | 0% helix, 0% strand | O00571 |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.75 | 0.79 | 73 | empty |
| 2 | 576 | 0.71 | 0.79 | 48 | empty |
| 3 | 606 | 0.69 | 0.78 | 54 | empty |
| 4 | 150 | 0.51 | 0.79 | 25 | empty |
| 5 | 142 | 0.48 | 0.78 | 23 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1312 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 1298 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 744 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 726 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 300 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4O2F · A peptide complexed with HLA-B*3901 · the same entry in another collection · chain F against F, 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
- O00571 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase DDX3X (O00571) · a predicted model of the same protein · chain F against A, TM-score 0.52
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 4O2F · PDBe 4O2F · UniProt P30475 · UniProt P61769 · UniProt O00571
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