Research workbench
Crystal structure of murine class II MHC I-ab in complex with a human clip peptide
Analyse Crystal structure of murine class II MHC I-ab in complex with a human clip… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MUJ
- Type
- protein
- Length
- 384 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class II histocompatibility antigen, a-B alpha chain; H-2 class II histocompatibility…
- UniProt
- P14434, P14483
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.43
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class II histocompatibility antigen, a-B alpha chain | protein | 185 | 15% helix, 44% strand | P14434 |
| B | H-2 class II histocompatibility antigen, a beta chain | protein | 184 | 21% helix, 44% strand | P14483 |
| C | Clip peptide | protein | 15 | 0% helix, 13% strand | — |
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
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 | 149 | 0.43 | 0.75 | 28 | empty |
| 2 | 97 | 0.39 | 0.76 | 20 | empty |
| 3 | 101 | 0.34 | 0.73 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2717 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 742 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 723 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1MUJ · Crystal structure of murine class II MHC I-Ab in complex with a human CLIP peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P14434 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a-B alpha… · a predicted model of the same protein · chain A against A, TM-score 0.92
- P14483 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a beta… · a predicted model of the same protein · chain B against A, TM-score 0.82
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 P14434
- Every structure of UniProt P14483
- Elsewhere: RCSB PDB 1MUJ · PDBe 1MUJ · UniProt P14434 · UniProt P14483
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