MolNFT v1 · #91895 · protein
Crystal structure of HLA-dm bound to HLA-DR1
4FQX · HLA class II histocompatibility antigen, dm alpha chain: “Crystal structure of HLA-dm bound to HLA-DR1”. X-ray diffraction, 1 ligand (NAG), 12 pockets (best druggability 0.71). MolNFT v1 #91895 on GenesisL1: 3D structure, binding…
- PDB
- 4FQX
- Type
- protein
- Length
- 751 residues
- Chains
- 5
- 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…
- UniProt
- P28067, P28068, P01903, P04229
- Ligands
- NAG
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 15% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | HLA class II histocompatibility antigen, dm alpha chain | protein | 186 | 16% helix, 46% strand | P28067 |
| D | HLA class II histocompatibility antigen, dm beta chain | protein | 191 | 14% helix, 40% strand | P28068 |
| E | Synthetic peptide | protein | 7 | 0% helix, 0% strand | — |
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 180 | 16% helix, 46% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-1 beta chain | protein | 187 | 16% helix, 42% strand | P04229 |
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
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.71 | 0.92 | 26 | empty |
| 2 | 479 | 0.71 | 0.81 | 53 | empty |
| 3 | 329 | 0.62 | 0.78 | 32 | empty |
| 4 | 281 | 0.57 | 0.77 | 39 | empty |
| 5 | 192 | 0.56 | 0.80 | 44 | empty |
Interfaces
7 interfaces between chains.
- C–D · 2799 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2603 Ų buried · 47 hydrogen bonds · protein-protein
- C–A · 1129 Ų buried · 16 hydrogen bonds · protein-protein
- D–B · 352 Ų buried · 5 hydrogen bonds · protein-protein
- D–A · 274 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4FQX · Crystal structure of HLA-DM bound to HLA-DR1 · the same entry in another collection · chain B against B, 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 C against A, TM-score 0.99
- P28068 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dm beta… · a predicted model of the same protein · chain D against A, TM-score 0.93
- P01903 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr alpha… · a predicted model of the same protein · chain A against A, TM-score 0.92
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
- Every structure of UniProt P01903
- Every structure of UniProt P04229
- Elsewhere: RCSB PDB 4FQX · PDBe 4FQX · UniProt P28067 · UniProt P28068 · UniProt P01903 · UniProt P04229
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