Research workbench
Crystal structure of non-phosphorylated form of RQA_V phosphopeptide bound to HLA-A2 in complex with LILRB1
Analyse Crystal structure of non-phosphorylated form of RQA_V phosphopeptide bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NO0
- Type
- protein
- Length
- 579 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin…
- UniProt
- P01892, P61769, P33241, Q8NHL6
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 24% helix, 40% strand | P01892 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 52% strand | P61769 |
| C | Lymphocyte-specific protein 1 | protein | 12 | 0% helix, 0% strand | P33241 |
| D | Leukocyte immunoglobulin-like receptor subfamily B member 1 | protein | 192 | 3% helix, 43% strand | Q8NHL6 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.76 | 0.79 | 91 | EDO |
| 2 | 547 | 0.69 | 0.79 | 55 | empty |
| 3 | 112 | 0.46 | 0.79 | 21 | empty |
| 4 | 68 | 0.41 | 0.80 | 17 | empty |
| 5 | 70 | 0.33 | 0.76 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1387 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 994 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 588 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 342 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4NO0 · Crystal structure of non-phosphorylated form of RQA_V phosphopeptide bound to HLA-A2 in… · 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
- Q8NHL6 · AlphaFold monomer V2.0 prediction for leukocyte immunoglobulin-like receptor subfamily B… · a predicted model of the same protein · chain D against A, TM-score 0.88
- P33241 · AlphaFold monomer V2.0 prediction for lymphocyte-specific protein 1 (P33241) · a predicted model of the same protein · chain C against A, TM-score 0.20
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 P01892
- Every structure of UniProt P61769
- Every structure of UniProt P33241
- Every structure of UniProt Q8NHL6
- Elsewhere: RCSB PDB 4NO0 · PDBe 4NO0 · UniProt P01892 · UniProt P61769 · UniProt P33241 · UniProt Q8NHL6
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