Research workbench
Histocompatibility antigen
Analyse Histocompatibility antigen in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FNE
- Type
- protein
- Length
- 790 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (MHC class II I-ek, alpha chain); Protein (MHC class II I-ek, beta chain)
- UniProt
- P04224, P02089
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Protein (MHC class II I-ek, alpha chain) | protein | 182 | 14% helix, 46% strand | P04224 |
| B, D | Protein (MHC class II I-ek, beta chain) | protein | 213 | 17% helix, 40% strand | P02089 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 683 | 0.84 | 0.88 | 95 | empty |
| 2 | 339 | 0.76 | 0.87 | 30 | empty |
| 3 | 378 | 0.75 | 0.86 | 29 | empty |
| 4 | 52 | 0.55 | 0.90 | 16 | empty |
| 5 | 63 | 0.54 | 0.88 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3443 Ų buried · 67 hydrogen bonds · protein-protein
- A–B · 3406 Ų buried · 66 hydrogen bonds · protein-protein
- B–D · 966 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 225 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 199 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1FNE · Histocompatibility antigen · the same entry in another collection · chain A against A, TM-score 1.00
- P04224 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, E-K alpha… · a predicted model of the same protein · chain A against A, TM-score 0.96
- P02089 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta-2 (P02089) · a predicted model of the same protein · chain B against A, TM-score 0.22
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 P04224
- Every structure of UniProt P02089
- Elsewhere: RCSB PDB 1FNE · PDBe 1FNE · UniProt P04224 · UniProt P02089
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