Research workbench
Crystal structure of duck MHC I for 2.06 ångström
Analyse Crystal structure of duck MHC I for 2.06 ångström in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GJX
- Type
- protein
- Length
- 379 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Arg-leu-ile-gln-asn-ser-ile-thr-ile
- UniProt
- Q6I7L2, Q14U75
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 266 | 29% helix, 40% strand | Q6I7L2 |
| B | Beta-2-microglobulin | protein | 104 | 0% helix, 47% strand | Q14U75 |
| C | Arg-leu-ile-gln-asn-ser-ile-thr-ile | protein | 9 | 0% helix, 0% strand | — |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.70 | 0.95 | 24 | empty |
| 2 | 489 | 0.65 | 0.77 | 52 | empty |
| 3 | 135 | 0.46 | 0.77 | 21 | empty |
| 4 | 69 | 0.39 | 0.79 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1645 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 914 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5GJX · Crystal structure of DUCK MHC I for 2.06 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 5GJX · PDBe 5GJX · UniProt Q6I7L2 · UniProt Q14U75
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