Research workbench
First insight into marsupial MHC I peptide presentation: immune features of lower mammals paralleled with bats
Analyse First insight into marsupial MHC I peptide presentation: immune features of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EDO
- Type
- protein
- Length
- 771 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Homo sapiens; Trichosurus vulpecula; SYNTHETIC CONSTRUCT
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Cys-asn-val-thr-leu-asn-tyr-pro
- UniProt
- Q95IT0, P61769
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.7 · 4 distinct chains · 16% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | MHC class I antigen | protein | 278 | 28% helix, 40% strand | Q95IT0 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | Cys-asn-val-thr-leu-asn-tyr-pro | protein | 8 | 0% helix, 0% strand | — |
| E | Beta-2-microglobulin | protein | 99 | 0% helix, 52% strand | P61769 |
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.73 | 0.98 | 21 | empty |
| 2 | 557 | 0.72 | 0.81 | 71 | empty |
| 3 | 741 | 0.71 | 0.78 | 57 | empty |
| 4 | 506 | 0.68 | 0.78 | 60 | empty |
| 5 | 528 | 0.67 | 0.77 | 49 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1434 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1383 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 839 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 795 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 252 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7EDO · First insight into marsupial MHC I peptide presentation: immune features of lower mammals… · 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 0.99
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 Q95IT0
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 7EDO · PDBe 7EDO · UniProt Q95IT0 · UniProt P61769
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