Research workbench
Crystal structure of HLA-B*2709 complexed with the glucagon receptor (gr) peptide (residues 412-420)
Analyse Crystal structure of HLA-B*2709 complexed with the glucagon receptor (gr)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CZF
- Type
- protein
- Length
- 384 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen; Beta-2-microglobulin; Glucagon receptor peptide
- UniProt
- P03989, P61769, P47871
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen | protein | 275 | 26% helix, 39% strand | P03989 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Glucagon receptor peptide | protein | 9 | 0% helix, 0% strand | P47871 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.67 | 0.78 | 45 | GOL |
| 2 | 147 | 0.51 | 0.80 | 21 | empty |
| 3 | 56 | 0.41 | 0.82 | 18 | empty |
| 4 | 57 | 0.37 | 0.80 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1339 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1091 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3CZF · Crystal structure of HLA-B*2709 complexed with the glucagon receptor (GR) peptide… · the same entry in another collection · chain A against A, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P47871 · AlphaFold monomer V2.0 prediction for glucagon receptor (P47871) · a predicted model of the same protein · chain C against A, TM-score 0.47
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 P03989
- Every structure of UniProt P61769
- Every structure of UniProt P47871
- Elsewhere: RCSB PDB 3CZF · PDBe 3CZF · UniProt P03989 · UniProt P61769 · UniProt P47871
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