Research workbench
Crystal structure of disulfide-linked HLA-G dimer
Analyse Crystal structure of disulfide-linked HLA-G dimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D31
- Type
- protein
- Length
- 747 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, alpha chain G; Beta-2-microglobulin; 9-mer…
- UniProt
- P17693, P61769, P16104
- Pockets
- 13 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, alpha chain G | protein | 269 | 26% helix, 36% strand | P17693 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 52% strand | P61769 |
| C, F | 9-mer peptide from histone H2A | protein | 9 | 0% helix, 0% strand | P16104 |
| D | HLA class I histocompatibility antigen, alpha chain G | protein | 262 | 27% helix, 35% strand | P17693 |
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.70 | 0.78 | 60 | empty |
| 2 | 578 | 0.68 | 0.78 | 46 | empty |
| 3 | 274 | 0.66 | 0.82 | 33 | empty |
| 4 | 198 | 0.52 | 0.78 | 27 | empty |
| 5 | 148 | 0.43 | 0.75 | 30 | empty |
Interfaces
6 interfaces between chains.
- D–E · 1372 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1349 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 974 Ų buried · 22 hydrogen bonds · protein-protein
- D–F · 971 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 171 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2D31 · Crystal structure of disulfide-linked HLA-G dimer · the same entry in another collection · chain F against F, 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
- P17693 · AlphaFold monomer V2.0 prediction for HLA class I histocompatibility antigen, alpha chain… · a predicted model of the same protein · chain A against A, TM-score 0.97
- P16104 · AlphaFold monomer V2.0 prediction for histone H2AX (P16104) · a predicted model of the same protein · chain C against A, TM-score 0.44
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 P17693
- Every structure of UniProt P61769
- Every structure of UniProt P16104
- Elsewhere: RCSB PDB 2D31 · PDBe 2D31 · UniProt P17693 · UniProt P61769 · UniProt P16104
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