MolNFT v1 · #83840 · protein
KIR3DL1 in complex with HLA-B*57:01.I80T
3WUW · HLA class I histocompatibility antigen, B-57 alpha chain: “KIR3DL1 in complex with HLA-B*57:01.I80T”. X-ray diffraction, 1 ligand (NAG), 10 pockets (best druggability 0.75). MolNFT v1 #83840 on GenesisL1: 3D structure, binding sites…
- PDB
- 3WUW
- Type
- protein
- Length
- 663 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; Peptide…
- UniProt
- P18465, P61769, P43629
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 44% 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 | 98 | 0% helix, 50% strand | P61769 |
| C | Peptide | protein | 9 | 0% helix, 0% strand | — |
| G | Killer cell immunoglobulin-like receptor 3DL1 | protein | 281 | 4% helix, 48% strand | P43629 |
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
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 587 | 0.75 | 0.82 | 63 | empty |
| 2 | 483 | 0.69 | 0.80 | 43 | empty |
| 3 | 172 | 0.58 | 0.81 | 26 | empty |
| 4 | 197 | 0.47 | 0.75 | 25 | empty |
| 5 | 75 | 0.44 | 0.81 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1381 Ų buried · 25 hydrogen bonds · protein-protein
- A–G · 980 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 834 Ų buried · 18 hydrogen bonds · protein-protein
- C–G · 71 Ų buried · 0 hydrogen bonds · protein-protein
- B–G · 43 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3WUW · KIR3DL1 in complex with HLA-B*57:01.I80T · 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 0.98
- 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 0.94
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 3WUW · PDBe 3WUW · UniProt P18465 · UniProt P61769 · UniProt P43629
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