Research workbench
KIR3DL1 in complex with HLA-B*57:01 presenting tsnlqeqigw
Analyse KIR3DL1 in complex with HLA-B*57:01 presenting tsnlqeqigw in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T70
- Type
- protein
- Length
- 672 residues
- Chains
- 4
- 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; Killer…
- UniProt
- P18465, P61769, P43629
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-57 alpha chain | protein | 275 | 27% helix, 39% strand | P18465 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| G | Killer cell immunoglobulin-like receptor 3DL1 | protein | 288 | 3% helix, 47% strand | P43629 |
| C | Decapeptide: thr-ser-asn-leu-gln-glu-gln-ile-gly-TRP | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.73 | 0.81 | 58 | empty |
| 2 | 528 | 0.71 | 0.80 | 47 | empty |
| 3 | 381 | 0.58 | 0.76 | 45 | empty |
| 4 | 53 | 0.41 | 0.82 | 17 | empty |
| 5 | 55 | 0.39 | 0.81 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1407 Ų buried · 25 hydrogen bonds · protein-protein
- A–G · 1000 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 863 Ų buried · 16 hydrogen bonds · protein-protein
- G–C · 189 Ų buried · 2 hydrogen bonds · protein-protein
- B–G · 52 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5T70 · KIR3DL1 in complex with HLA-B*57:01 presenting TSNLQEQIGW · 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 0.99
- P43629 · AlphaFold monomer V2.0 prediction for killer cell immunoglobulin-like receptor 3DL1… · a predicted model of the same protein · chain G against A, TM-score 0.93
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 P43629
- Elsewhere: RCSB PDB 5T70 · PDBe 5T70 · UniProt P18465 · UniProt P61769 · UniProt P43629
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