MolNFT v1 · #31965 · protein
Crystal structure of HLA-dm
2BC4 · HLA class II histocompatibility antigen, dm alpha chain: “Crystal structure of HLA-dm”. X-ray diffraction, 4 ligands (BMA, NAG, NDG), 11 pockets (best druggability 0.65). MolNFT v1 #31965 on GenesisL1: 3D structure, binding sites…
- PDB
- 2BC4
- Type
- protein
- Length
- 771 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dm alpha chain; HLA class II histocompatibility…
- Ligands
- BMA, NAG, NDG, CL
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dm alpha chain | protein | 188 | 12% helix, 47% strand | — |
| B | HLA class II histocompatibility antigen, dm beta chain | protein | 191 | 19% helix, 43% strand | — |
| C | HLA class II histocompatibility antigen, dm alpha chain | protein | 195 | 14% helix, 47% strand | — |
| D | HLA class II histocompatibility antigen, dm beta chain | protein | 197 | 22% helix, 42% strand | — |
Ligands and binding sites
- BMA · beta-D-mannopyranose · sugar · 4 copies
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B, C, D
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains B, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.65 | 0.86 | 28 | CL |
| 2 | 141 | 0.61 | 0.85 | 29 | CL |
| 3 | 198 | 0.53 | 0.78 | 24 | empty |
| 4 | 192 | 0.52 | 0.77 | 25 | empty |
| 5 | 135 | 0.44 | 0.76 | 22 | empty |
Interfaces
2 interfaces between chains.
- C–D · 3116 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 2822 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2BC4 · Crystal structure of HLA-DM · 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
- Elsewhere: RCSB PDB 2BC4 · PDBe 2BC4
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