Research workbench
Giant panda MHC class I complexes
Analyse Giant panda MHC class I complexes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DC6
- Type
- protein
- Length
- 765 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Ccv-NGY9 peptide from spike protein
- UniProt
- B2KT53, D2GW37, Q65984
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | MHC class I antigen | protein | 275 | 24% helix, 39% strand | B2KT53 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | D2GW37 |
| D | Beta-2-microglobulin | protein | 98 | 0% helix, 52% strand | D2GW37 |
| E, F | Ccv-NGY9 peptide from spike protein | protein | 9 | 0% helix, 0% strand | Q65984 |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 588 | 0.73 | 0.81 | 70 | empty |
| 2 | 479 | 0.66 | 0.78 | 48 | empty |
| 3 | 402 | 0.66 | 0.79 | 47 | empty |
| 4 | 160 | 0.57 | 0.82 | 38 | empty |
| 5 | 127 | 0.51 | 0.80 | 20 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1396 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1291 Ų buried · 21 hydrogen bonds · protein-protein
- C–F · 1015 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 950 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 322 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7DC6 · Giant panda MHC class I complexes · 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 B2KT53
- Every structure of UniProt D2GW37
- Every structure of UniProt Q65984
- Elsewhere: RCSB PDB 7DC6 · PDBe 7DC6 · UniProt B2KT53 · UniProt D2GW37 · UniProt Q65984
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