Research workbench
Mooring stone-like ARG114 pulls diverse bulged peptides: first insight into african swine fever virus-derived T cell epitopes presented by swine major histocompatibility complex class I
Analyse Mooring stone-like ARG114 pulls diverse bulged peptides: first insight into… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EMD
- Type
- protein
- Length
- 382 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucocyte antigen; Beta-2-microglobulin; Tyr-gly-asp-phe-phe-his-asp-met-val
- UniProt
- O19075, Q07717
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucocyte antigen | protein | 275 | 27% helix, 40% strand | O19075 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | Q07717 |
| C | Tyr-gly-asp-phe-phe-his-asp-met-val | protein | 9 | 0% helix, 0% strand | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 621 | 0.69 | 0.78 | 54 | empty |
| 2 | 150 | 0.46 | 0.77 | 21 | empty |
| 3 | 50 | 0.27 | 0.75 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1422 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 907 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7EMD · Mooring Stone-Like Arg114 Pulls Diverse Bulged Peptides: First Insight into African Swine… · the same entry in another collection · chain A against A, TM-score 1.00
- Q07717 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (Q07717) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O19075
- Every structure of UniProt Q07717
- Elsewhere: RCSB PDB 7EMD · PDBe 7EMD · UniProt O19075 · UniProt Q07717
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