Research workbench
Crystal structure of class II MHC molecule iek bound to moth cytochrome C peptide
Analyse Crystal structure of class II MHC molecule iek bound to moth cytochrome C… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KT2
- Type
- protein
- Length
- 790 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class II histocompatibility antigen, E-D alpha chain; Fusion protein consisting of…
- UniProt
- P01904
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | H-2 class II histocompatibility antigen, E-D alpha chain | protein | 182 | 14% helix, 47% strand | P01904 |
| B, D | Fusion protein consisting of cytochrome C peptide, glycine rich linker, and MHC E-beta-K | protein | 213 | 17% helix, 38% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 715 | 0.85 | 0.89 | 100 | empty |
| 2 | 284 | 0.77 | 0.89 | 30 | empty |
| 3 | 244 | 0.75 | 0.89 | 31 | empty |
| 4 | 116 | 0.54 | 0.83 | 22 | empty |
| 5 | 169 | 0.45 | 0.75 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3467 Ų buried · 66 hydrogen bonds · protein-protein
- C–D · 3467 Ų buried · 62 hydrogen bonds · protein-protein
- B–D · 969 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 262 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 250 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 1KT2 · Crystal structure of class II MHC molecule iek bound to moth cytochrome C peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P01904 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, E-D alpha… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P01904
- Elsewhere: RCSB PDB 1KT2 · PDBe 1KT2 · UniProt P01904
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