Research workbench
Natural killer cell receptor nkr-P1B from rattus norvegicus in complex with its cognate ligand clr-11
Analyse Natural killer cell receptor nkr-P1B from rattus norvegicus in complex with its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ODU
- Type
- protein
- Length
- 372 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-type lectin domain family 2 member D11; Killer cell lectin-like receptor subfamily B…
- UniProt
- Q0H8B9, A4KWA1
- Ligands
- NAG, ZN
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-type lectin domain family 2 member D11 | protein | 129 | 16% helix, 29% strand | Q0H8B9 |
| B | C-type lectin domain family 2 member D11 | protein | 122 | 16% helix, 31% strand | Q0H8B9 |
| C | Killer cell lectin-like receptor subfamily B member 1B allele a | protein | 121 | 18% helix, 39% strand | A4KWA1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, C, B
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.41 | 0.78 | 17 | empty |
| 2 | 87 | 0.38 | 0.77 | 12 | empty |
| 3 | 67 | 0.30 | 0.74 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1115 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 868 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 7ODU · Natural killer cell receptor NKR-P1B from Rattus norvegicus in complex with its cognate… · the same entry in another collection · chain A against A, TM-score 1.00
- Q0H8B9 · AlphaFold monomer V2.0 prediction for C-type lectin domain family 2 member D11 (Q0H8B9) · a predicted model of the same protein · chain B against A, TM-score 0.96
- A4KWA1 · AlphaFold monomer V2.0 prediction for killer cell lectin-like receptor subfamily B member… · a predicted model of the same protein · chain C 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 Q0H8B9
- Every structure of UniProt A4KWA1
- Elsewhere: RCSB PDB 7ODU · PDBe 7ODU · UniProt Q0H8B9 · UniProt A4KWA1
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