MolNFT v1 · #160097 · protein
Killer cell immunoglobulin-like receptor 2DL3 in complex with HLA- C*07:02
6PAG · HLA class I histocompatibility antigen, cw-7 alpha chain: “Killer cell immunoglobulin-like receptor 2DL3 in complex with HLA- C*07:02”. X-ray diffraction, 6 pockets (best druggability 0.66). MolNFT v1 #160097 on GenesisL1: 3D…
- PDB
- 6PAG
- Type
- protein
- Length
- 553 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, cw-7 alpha chain; Beta-2-microglobulin…
- UniProt
- P10321, P61769, P43628
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, cw-7 alpha chain | protein | 277 | 29% helix, 38% strand | P10321 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Arg-tyr-arg-pro-gly-thr-val-ala-leu | protein | 9 | 0% helix, 0% strand | — |
| D | Killer cell immunoglobulin-like receptor 2DL3 | protein | 167 | 2% helix, 49% strand | P43628 |
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 | 525 | 0.66 | 0.77 | 53 | empty |
| 2 | 183 | 0.54 | 0.79 | 27 | empty |
| 3 | 154 | 0.50 | 0.79 | 22 | empty |
| 4 | 112 | 0.50 | 0.81 | 19 | empty |
| 5 | 58 | 0.29 | 0.74 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1500 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 932 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 724 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 97 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6PAG · Killer cell immunoglobulin-like receptor 2DL3 in complex with HLA-C*07:02 · 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 0.97
- P10321 · AlphaFold monomer V2.0 prediction for HLA class I histocompatibility antigen, C alpha… · a predicted model of the same protein · chain A against A, TM-score 0.97
- P43628 · AlphaFold monomer V2.0 prediction for killer cell immunoglobulin-like receptor 2DL3… · a predicted model of the same protein · chain D against A, TM-score 0.96
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 P10321
- Every structure of UniProt P61769
- Every structure of UniProt P43628
- Elsewhere: RCSB PDB 6PAG · PDBe 6PAG · UniProt P10321 · UniProt P61769 · UniProt P43628
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