Research workbench
Model of MHC class I H2-M3 with nonapeptide from rat ND1 refined at 2.3 ångströms resolution
Analyse Model of MHC class I H2-M3 with nonapeptide from rat ND1 refined at 2.3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MHC
- Type
- protein
- Length
- 768 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen H2-M3; Nonapeptide from rat NADH dehydrogenase
- UniProt
- Q31093, P01887, P03889
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | MHC class I antigen H2-M3 | protein | 276 | 26% helix, 40% strand | Q31093 |
| B, E | MHC class I antigen H2-M3 | protein | 99 | 0% helix, 52% strand | P01887 |
| C, F | Nonapeptide from rat NADH dehydrogenase | protein | 9 | 0% helix, 0% strand | P03889 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.81 | 0.83 | 110 | empty |
| 2 | 606 | 0.66 | 0.76 | 61 | empty |
| 3 | 589 | 0.66 | 0.76 | 57 | empty |
| 4 | 55 | 0.38 | 0.80 | 18 | empty |
| 5 | 68 | 0.36 | 0.77 | 14 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1319 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1290 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 880 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 861 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 470 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 modified, 1 glycan (disulfide, formylation, N-glycosylation).
Compared structures
- 1MHC · Model of MHC class I H2-M3 with nonapeptide from rat ND1 refined at 2.3 ångströms… · the same entry in another collection · chain F against F, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P03889 · AlphaFold monomer V2.0 prediction for NADH-ubiquinone oxidoreductase chain 1 (P03889) · a predicted model of the same protein · chain C against A, TM-score 0.33
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 Q31093
- Every structure of UniProt P01887
- Every structure of UniProt P03889
- Elsewhere: RCSB PDB 1MHC · PDBe 1MHC · UniProt Q31093 · UniProt P01887 · UniProt P03889
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