MolNFT v1 · #70527 · protein
Crystal structure of HLA-B*4104 in complex with a 11MER self-peptide derived from S-methyl-5-thioadenosine phosphorylase
3LN5 · HLA class I histocompatibility antigen, B-41 alpha chain: “Crystal structure of HLA-B*4104 in complex with a 11MER self-peptide derived from S-methyl-5-thioadenosine…”. X-ray diffraction, 3 pockets (best druggability 0.68). MolNFT…
- PDB
- 3LN5
- 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-41 alpha chain; Beta-2-microglobulin; 11-mer…
- UniProt
- P30479, P61769, Q13126
- Pockets
- 3 · 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-41 alpha chain | protein | 274 | 27% helix, 39% strand | P30479 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | 11-mer peptide from S-methyl-5'-thioadenosine phosphorylase | protein | 11 | 27% helix, 0% strand | Q13126 |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.68 | 0.77 | 55 | empty |
| 2 | 217 | 0.52 | 0.77 | 40 | empty |
| 3 | 87 | 0.42 | 0.79 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1294 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 973 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3LN5 · Crystal structure of HLA-B*4104 in complex with a 11mer self-peptide derived from… · 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
- Q13126 · AlphaFold monomer V2.0 prediction for S-methyl-5'-thioadenosine phosphorylase (Q13126) · a predicted model of the same protein · chain C against A, TM-score 0.43
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 P30479
- Every structure of UniProt P61769
- Every structure of UniProt Q13126
- Elsewhere: RCSB PDB 3LN5 · PDBe 3LN5 · UniProt P30479 · UniProt P61769 · UniProt Q13126
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