Research workbench
KIR3DL1 in complex with HLA-B*5701
Analyse KIR3DL1 in complex with HLA-B*5701 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VH8
- Type
- protein
- Length
- 1,311 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-57 alpha chain; Beta-2-microglobulin; Peptide…
- UniProt
- P18465, P61769, P01834, P43629
- Ligands
- NAG
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen, B-57 alpha chain | protein | 275 | 27% helix, 39% strand | P18465 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C, F | Peptide of ig kappa chain C region | protein | 9 | 0% helix, 0% strand | P01834 |
| G | Killer cell immunoglobulin-like receptor 3DL1 | protein | 281 | 4% helix, 47% strand | P43629 |
| H | Killer cell immunoglobulin-like receptor 3DL1 | protein | 264 | 4% helix, 47% strand | P43629 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 682 | 0.73 | 0.80 | 69 | empty |
| 2 | 573 | 0.72 | 0.80 | 57 | empty |
| 3 | 492 | 0.70 | 0.80 | 42 | empty |
| 4 | 474 | 0.70 | 0.80 | 46 | empty |
| 5 | 212 | 0.62 | 0.82 | 34 | empty |
Interfaces
12 interfaces between chains.
- D–E · 1430 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1428 Ų buried · 24 hydrogen bonds · protein-protein
- A–G · 938 Ų buried · 12 hydrogen bonds · protein-protein
- D–H · 927 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 829 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 3VH8 · KIR3DL1 in complex with HLA-B*5701 · the same entry in another collection · chain H against H, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain E against A, TM-score 0.98
- P43629 · AlphaFold monomer V2.0 prediction for killer cell immunoglobulin-like receptor 3DL1… · a predicted model of the same protein · chain H against A, TM-score 0.95
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 P18465
- Every structure of UniProt P61769
- Every structure of UniProt P01834
- Every structure of UniProt P43629
- Elsewhere: RCSB PDB 3VH8 · PDBe 3VH8 · UniProt P18465 · UniProt P61769 · UniProt P01834 · UniProt P43629
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