Research workbench
'porcine (sus scrofa) major histocompatibility complex, class I, with human BETA2 micro globulin, presenting efedltfla
Analyse 'porcine (sus scrofa) major histocompatibility complex, class I, with human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NQ3
- Type
- protein
- Length
- 770 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Glu-phe-glu-asp-leu-thr-phe-leu-ala
- UniProt
- B1PJV3, P61769
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | MHC class I antigen | protein | 276 | 28% helix, 39% strand | B1PJV3 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 50% strand | P61769 |
| C, F | Glu-phe-glu-asp-leu-thr-phe-leu-ala | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, D, E
- GOL · Glycerol · additive · 2 copies · chains D, E
- EDO · 1,2-ethanediol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.82 | 0.86 | 88 | empty |
| 2 | 717 | 0.81 | 0.85 | 80 | EDO |
| 3 | 206 | 0.67 | 0.85 | 35 | empty |
| 4 | 120 | 0.58 | 0.85 | 24 | empty |
| 5 | 95 | 0.49 | 0.82 | 20 | empty |
Interfaces
8 interfaces between chains.
- A–D · 1417 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 1408 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1386 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 850 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 837 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5NQ3 · 'Porcine (Sus scrofa) Major Histocompatibility Complex, class I, with human beta2 micro… · 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 0.98
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 B1PJV3
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 5NQ3 · PDBe 5NQ3 · UniProt B1PJV3 · UniProt P61769
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