MolNFT v1 · #179520 · protein
KIR3DL1*005 in complex with HLA-A*24:02 presenting the rypltfgw peptide
7K81 · MHC class I antigen: “KIR3DL1*005 in complex with HLA-A*24:02 presenting the rypltfgw peptide”. X-ray diffraction, 1 ligand (NAG), 6 pockets (best druggability 0.74). MolNFT v1 #179520 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7K81
- Type
- protein
- Length
- 664 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Arg-tyr-pro-leu-thr-phe-gly-TRP; KIR3DL1
- UniProt
- A0A411J078, P61769, I6LEL9
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 276 | 27% helix, 40% strand | A0A411J078 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 51% strand | P61769 |
| C | Arg-tyr-pro-leu-thr-phe-gly-TRP | protein | 8 | 0% helix, 0% strand | — |
| G | KIR3DL1 | protein | 280 | 4% helix, 48% strand | I6LEL9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 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 | 753 | 0.74 | 0.79 | 64 | empty |
| 2 | 596 | 0.67 | 0.77 | 52 | empty |
| 3 | 491 | 0.62 | 0.76 | 45 | empty |
| 4 | 141 | 0.60 | 0.84 | 29 | empty |
| 5 | 52 | 0.38 | 0.80 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1398 Ų buried · 22 hydrogen bonds · protein-protein
- A–G · 991 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 943 Ų buried · 19 hydrogen bonds · protein-protein
- C–G · 63 Ų buried · 0 hydrogen bonds · protein-protein
- B–G · 43 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7K81 · KIR3DL1*005 in complex with HLA-A*24:02 presenting the RYPLTFGW peptide · 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
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 A0A411J078
- Every structure of UniProt P61769
- Every structure of UniProt I6LEL9
- Elsewhere: RCSB PDB 7K81 · PDBe 7K81 · UniProt A0A411J078 · UniProt P61769 · UniProt I6LEL9
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