Research workbench
Histocompatibility antigen HLA-dm
Analyse Histocompatibility antigen HLA-dm in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HDM
- Type
- protein
- Length
- 367 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (class II histocompatibility antigen, M alpha chain); Protein (class II…
- UniProt
- P28067, P28068
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (class II histocompatibility antigen, M alpha chain) | protein | 184 | 11% helix, 47% strand | P28067 |
| B | Protein (class II histocompatibility antigen, M beta chain) | protein | 183 | 17% helix, 44% strand | P28068 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.65 | 0.88 | 24 | empty |
| 2 | 201 | 0.54 | 0.78 | 25 | empty |
| 3 | 118 | 0.41 | 0.76 | 19 | empty |
| 4 | 55 | 0.32 | 0.77 | 17 | empty |
| 5 | 65 | 0.30 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2755 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1HDM · Histocompatibility antigen HLA-dm · the same entry in another collection · chain A against A, TM-score 1.00
- P28067 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dm alpha… · a predicted model of the same protein · chain A against A, TM-score 0.98
- P28068 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dm beta… · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P28067
- Every structure of UniProt P28068
- Elsewhere: RCSB PDB 1HDM · PDBe 1HDM · UniProt P28067 · UniProt P28068
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