MolNFT v1 · #114139 · protein
KIR3DL1*005 in complex with HLA-B*57:01
5B38 · HLA class I histocompatibility antigen, B-57 alpha chain: “KIR3DL1*005 in complex with HLA-B*57:01”. X-ray diffraction, 1 ligand (NAG), 8 pockets (best druggability 0.72). MolNFT v1 #114139 on GenesisL1: 3D structure, binding sites…
- PDB
- 5B38
- Type
- protein
- Length
- 656 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
- 8 · 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 | 27% helix, 40% strand | P18465 |
| B | Beta-2-microglobulin | protein | 99 | 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 | 273 | 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
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.72 | 0.80 | 59 | empty |
| 2 | 530 | 0.68 | 0.79 | 52 | empty |
| 3 | 139 | 0.67 | 0.88 | 36 | empty |
| 4 | 319 | 0.55 | 0.75 | 44 | empty |
| 5 | 83 | 0.45 | 0.81 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1376 Ų buried · 23 hydrogen bonds · protein-protein
- A–G · 982 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 822 Ų buried · 18 hydrogen bonds · protein-protein
- C–G · 101 Ų buried · 0 hydrogen bonds · protein-protein
- B–G · 46 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5B38 · KIR3DL1*005 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 0.98
- 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 0.93
- P01834 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01834) · a predicted model of the same protein · chain C against A, TM-score 0.45
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 5B38 · PDBe 5B38 · UniProt P18465 · UniProt P61769 · UniProt P01834 · UniProt P43629
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