MolNFT v1 · #119931 · protein
Crystal structure of duck MHC class I for 1.71 ångström
5GJY · MHC class I antigen: “Crystal structure of duck MHC class I for 1.71 ångström”. X-ray diffraction, 3 pockets (best druggability 0.65). MolNFT v1 #119931 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GJY
- Type
- protein
- Length
- 373 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Met-val-met-glu-leu-ile-arg-met-ile
- UniProt
- Q6I7L2, Q14U75
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 266 | 29% helix, 41% strand | Q6I7L2 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | Q14U75 |
| C | Met-val-met-glu-leu-ile-arg-met-ile | protein | 7 | 0% helix, 0% strand | — |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.65 | 0.77 | 52 | empty |
| 2 | 51 | 0.54 | 0.89 | 20 | empty |
| 3 | 125 | 0.45 | 0.77 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1590 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 862 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5GJY · Crystal structure of DUCK MHC CLASS I for 1.71 angstrom · the same entry in another collection · chain A against A, TM-score 1.00
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 Q6I7L2
- Every structure of UniProt Q14U75
- Elsewhere: RCSB PDB 5GJY · PDBe 5GJY · UniProt Q6I7L2 · UniProt Q14U75
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