MolNFT v1 · #25132 · protein
The crystal structure of class I major histocompatibility complex, H-2KD at 2.0 a resolution
1VGK · H-2 class I histocompatibility antigen, K-D alpha chain: “The crystal structure of class I major histocompatibility complex, H-2KD at 2.0 a resolution”. X-ray diffraction, 5 pockets (best druggability 0.68). MolNFT v1 #25132 on…
- PDB
- 1VGK
- Type
- protein
- Length
- 382 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, K-D alpha chain; Beta-2-microglobulin; Syvntnmgl
- UniProt
- P01902, P61769
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, K-D alpha chain | protein | 274 | 29% helix, 39% strand | P01902 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Syvntnmgl | protein | 9 | 0% helix, 0% strand | — |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.68 | 0.77 | 55 | empty |
| 2 | 105 | 0.44 | 0.78 | 22 | empty |
| 3 | 98 | 0.39 | 0.76 | 23 | empty |
| 4 | 87 | 0.37 | 0.76 | 16 | empty |
| 5 | 56 | 0.31 | 0.76 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1320 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 916 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1VGK · The crystal structure of class I Major histocompatibility complex, H-2Kd at 2.0 A… · the same entry in another collection · chain A against A, 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
- P01902 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, K-D alpha… · a predicted model of the same protein · chain A 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 P01902
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 1VGK · PDBe 1VGK · UniProt P01902 · UniProt P61769
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