MolNFT v1 · #114140 · protein
KIR3DL1*015 in complex with HLA-B*57:01
5B39 · HLA class I histocompatibility antigen, B-57 alpha chain: “KIR3DL1*015 in complex with HLA-B*57:01”. X-ray diffraction, 1 ligand (NAG), 6 pockets (best druggability 0.72). MolNFT v1 #114140 on GenesisL1: 3D structure, binding sites…
- PDB
- 5B39
- Type
- protein
- Length
- 659 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, P01834, P43629
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.72
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 | 28% helix, 40% strand | P18465 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 52% strand | P61769 |
| C | Peptide from ig kappa chain C region | protein | 9 | 0% helix, 0% strand | P01834 |
| G | Killer cell immunoglobulin-like receptor 3DL1 | protein | 277 | 3% helix, 47% 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
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.72 | 0.80 | 59 | empty |
| 2 | 478 | 0.69 | 0.80 | 42 | empty |
| 3 | 117 | 0.61 | 0.87 | 27 | empty |
| 4 | 282 | 0.51 | 0.74 | 36 | empty |
| 5 | 58 | 0.39 | 0.80 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1388 Ų buried · 26 hydrogen bonds · protein-protein
- A–G · 1084 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 832 Ų buried · 20 hydrogen bonds · protein-protein
- C–G · 105 Ų buried · 0 hydrogen bonds · protein-protein
- B–G · 55 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5B39 · KIR3DL1*015 in complex with HLA-B*57:01 · 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 0.94
- P01834 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01834) · a predicted model of the same protein · chain C against A, TM-score 0.44
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 5B39 · PDBe 5B39 · UniProt P18465 · UniProt P61769 · UniProt P01834 · UniProt P43629
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