Research workbench
Structural and functional basis for HLA-G isoform recognition of immune checkpoint receptor lilrbs
Analyse Structural and functional basis for HLA-G isoform recognition of immune… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K60
- Type
- protein
- Length
- 973 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, alpha chain G; Beta-2-microglobulin; Peptide from…
- UniProt
- P17693, P61769, A0A0U1RRH7, A0A0G2JQ44
- Ligands
- IOD
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 19% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, alpha chain G | protein | 257 | 28% helix, 37% strand | P17693 |
| B, F | Beta-2-microglobulin | protein | 100 | 0% helix, 51% strand | P61769 |
| C, G | Peptide from histone H2A.J | protein | 9 | 0% helix, 0% strand | A0A0U1RRH7 |
| D | Leukocyte immunoglobulin-like receptor subfamily B member 1 | protein | 141 | 9% helix, 38% strand | A0A0G2JQ44 |
| E | HLA class I histocompatibility antigen, alpha chain G | protein | 274 | 26% helix, 41% strand | P17693 |
| H | Leukocyte immunoglobulin-like receptor subfamily B member 1 | protein | 83 | 8% helix, 30% strand | A0A0G2JQ44 |
Ligands and binding sites
- IOD · Iodide ion · ion · 8 copies · chains A, F, B, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 886 | 0.79 | 0.82 | 90 | empty |
| 2 | 1033 | 0.78 | 0.80 | 84 | empty |
| 3 | 764 | 0.77 | 0.82 | 66 | empty |
| 4 | 1116 | 0.77 | 0.79 | 81 | IOD |
| 5 | 79 | 0.50 | 0.84 | 21 | empty |
Interfaces
11 interfaces between chains.
- E–F · 1406 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1374 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 999 Ų buried · 20 hydrogen bonds · protein-protein
- E–G · 972 Ų buried · 20 hydrogen bonds · protein-protein
- F–H · 741 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6K60 · Structural and functional basis for HLA-G isoform recognition of immune checkpoint… · the same entry in another collection · chain H against H, TM-score 1.00
- P17693 · AlphaFold monomer V2.0 prediction for HLA class I histocompatibility antigen, alpha chain… · a predicted model of the same protein · chain E against A, TM-score 0.99
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 A0A0U1RRH7
- Every structure of UniProt A0A0G2JQ44
- Elsewhere: RCSB PDB 6K60 · PDBe 6K60 · UniProt P17693 · UniProt P61769 · UniProt A0A0U1RRH7 · UniProt A0A0G2JQ44
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