Research workbench
Crystal structure of the autoimmune MHC class II I-au complexed with myelin basic protein 1-11 at 2.2A
Analyse Crystal structure of the autoimmune MHC class II I-au complexed with myelin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K2D
- Type
- protein
- Length
- 379 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class II histocompatibility antigen, a-U alpha chain; H-2 class II histocompatibility…
- UniProt
- P14438, P06344
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class II histocompatibility antigen, a-U alpha chain | protein | 182 | 14% helix, 45% strand | P14438 |
| B | H-2 class II histocompatibility antigen, a-U beta chain | protein | 185 | 18% helix, 46% strand | P06344 |
| P | Myelin basic protein peptide with 8 residue linker peptide | protein | 12 | 0% helix, 8% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 208 | 0.48 | 0.75 | 27 | empty |
| 2 | 135 | 0.43 | 0.75 | 18 | empty |
| 3 | 115 | 0.40 | 0.76 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2622 Ų buried · 49 hydrogen bonds · protein-protein
- B–P · 686 Ų buried · 11 hydrogen bonds · protein-protein
- A–P · 508 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 1K2D · Crystal structure of the autoimmune MHC class II I-Au complexed with myelin basic protein… · the same entry in another collection · chain A against A, TM-score 1.00
- P14438 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a-U alpha… · a predicted model of the same protein · chain A against A, TM-score 0.98
- P06344 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a-U beta… · a predicted model of the same protein · chain B against A, TM-score 0.89
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 P14438
- Every structure of UniProt P06344
- Elsewhere: RCSB PDB 1K2D · PDBe 1K2D · UniProt P14438 · UniProt P06344
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