Research workbench
Crystal structure of non-phosphorylated form of rtf phosphopeptide bound to HLA-A2 in complex with LILRB1
Analyse Crystal structure of non-phosphorylated form of rtf 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
- 6EWO
- Type
- protein
- Length
- 1,126 residues
- Chains
- 8
- 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; Synemin…
- UniProt
- P01892, P61769, O15061, D9IDM8
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 16% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 26% helix, 39% strand | P01892 |
| B, F | Beta-2-microglobulin | protein | 99 | 0% helix, 52% strand | P61769 |
| C, G | Synemin | protein | 9 | 0% helix, 0% strand | O15061 |
| D | Lir-1 | protein | 184 | 5% helix, 44% strand | D9IDM8 |
| E | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 274 | 27% helix, 40% strand | P01892 |
| H | Lir-1 | protein | 176 | 6% helix, 42% strand | D9IDM8 |
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.77 | 0.79 | 75 | empty |
| 2 | 876 | 0.76 | 0.80 | 66 | empty |
| 3 | 545 | 0.67 | 0.78 | 46 | empty |
| 4 | 595 | 0.67 | 0.77 | 60 | empty |
| 5 | 526 | 0.67 | 0.78 | 58 | empty |
Interfaces
9 interfaces between chains.
- E–F · 1417 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1351 Ų buried · 19 hydrogen bonds · protein-protein
- E–G · 897 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 884 Ų buried · 15 hydrogen bonds · protein-protein
- F–H · 651 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6EWO · Crystal structure of non-phosphorylated form of RTF PHOSPHOPEPTIDE BOUND TO HLA-A2 in… · the same entry in another collection · chain H against H, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain F against A, TM-score 0.98
- O15061 · AlphaFold monomer V2.0 prediction for synemin (O15061) · a predicted model of the same protein · chain C against A, TM-score 0.33
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 O15061
- Every structure of UniProt D9IDM8
- Elsewhere: RCSB PDB 6EWO · PDBe 6EWO · UniProt P01892 · UniProt P61769 · UniProt O15061 · UniProt D9IDM8
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