Research workbench
MHC class I H-2DB complexed with glycopeptide K3G
Analyse MHC class I H-2DB complexed with glycopeptide K3G in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QLF
- Type
- protein
- Length
- 384 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I H-2DB heavy chain; Human beta-2-microglobulin; Synthetic glycopeptide
- UniProt
- P01899, P01884, P04857
- Ligands
- NAG, SO4
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I H-2DB heavy chain | protein | 276 | 26% helix, 39% strand | P01899 |
| B | Human beta-2-microglobulin | protein | 99 | 0% helix, 52% strand | P01884 |
| C | Synthetic glycopeptide | protein | 9 | 0% helix, 0% strand | P04857 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A, C
- SO4 · Sulfate ion · ion · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 662 | 0.68 | 0.76 | 58 | GOL |
| 2 | 83 | 0.44 | 0.80 | 18 | empty |
| 3 | 109 | 0.42 | 0.77 | 19 | empty |
| 4 | 136 | 0.41 | 0.75 | 28 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1286 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 869 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, O-glycosylation).
Compared structures
- 1QLF · MHC class I H-2DB complexed with glycopeptide K3G · the same entry in another collection · chain A against A, TM-score 1.00
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 P01899
- Every structure of UniProt P01884
- Every structure of UniProt P04857
- Elsewhere: RCSB PDB 1QLF · PDBe 1QLF · UniProt P01899 · UniProt P01884 · UniProt P04857
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