MolNFT v1 · #12159 · protein
Crystal structure of mouse H2-dm
1K8I · MHC class II H2-M alpha chain: “Crystal structure of mouse H2-dm”. X-ray diffraction, 1 ligand (NAG), 4 pockets (best druggability 0.60). MolNFT v1 #12159 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1K8I
- Type
- protein
- Length
- 371 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class II H2-M alpha chain; MHC class II H2-M beta 2 chain
- UniProt
- P28078, Q31099
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class II H2-M alpha chain | protein | 181 | 14% helix, 48% strand | P28078 |
| B | MHC class II H2-M beta 2 chain | protein | 190 | 19% helix, 43% strand | Q31099 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 115 | 0.60 | 0.86 | 23 | empty |
| 2 | 271 | 0.60 | 0.79 | 27 | empty |
| 3 | 120 | 0.41 | 0.76 | 22 | empty |
| 4 | 57 | 0.27 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2685 Ų buried · 50 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
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 P28078
- Every structure of UniProt Q31099
- Elsewhere: RCSB PDB 1K8I · PDBe 1K8I · UniProt P28078 · UniProt Q31099
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