MolNFT v1 · #35033 · protein
Crystal structure of LILRB2(LIR2/ILT4/CD85D) complexed with HLA-G
2DYP · HLA class I histocompatibility antigen, alpha chain G: “Crystal structure of LILRB2(LIR2/ILT4/CD85D) complexed with HLA-G”. X-ray diffraction, 9 pockets (best druggability 0.75). MolNFT v1 #35033 on GenesisL1: 3D structure, binding…
- PDB
- 2DYP
- Type
- protein
- Length
- 569 residues
- Chains
- 4
- 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, Q8N423
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, alpha chain G | protein | 275 | 26% helix, 39% strand | P17693 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 51% strand | P61769 |
| C | 9 mer peptide from histone H2A.X | protein | 9 | 0% helix, 0% strand | P16104 |
| D | Leukocyte immunoglobulin-like receptor subfamily B member 2 | protein | 185 | 3% helix, 47% strand | Q8N423 |
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 886 | 0.75 | 0.79 | 56 | empty |
| 2 | 577 | 0.66 | 0.76 | 50 | empty |
| 3 | 122 | 0.42 | 0.76 | 23 | empty |
| 4 | 52 | 0.40 | 0.82 | 17 | empty |
| 5 | 122 | 0.38 | 0.74 | 23 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1411 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 992 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 677 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 502 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2DYP · Crystal Structure of LILRB2(LIR2/ILT4/CD85d) complexed with HLA-G · the same entry in another collection · chain D against D, 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 0.99
- 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 0.98
- Q8N423 · AlphaFold monomer V2.0 prediction for leukocyte immunoglobulin-like receptor subfamily B… · a predicted model of the same protein · chain D against A, TM-score 0.95
- P16104 · AlphaFold monomer V2.0 prediction for histone H2AX (P16104) · a predicted model of the same protein · chain C against A, TM-score 0.40
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
- Every structure of UniProt Q8N423
- Elsewhere: RCSB PDB 2DYP · PDBe 2DYP · UniProt P17693 · UniProt P61769 · UniProt P16104 · UniProt Q8N423
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