MolNFT v1 · #153599 · protein
Trimeric structure of kupffer cell C-type lectin receptor CLEC4F
6JJJ · C-type lectin domain family 4 member F: “Trimeric structure of kupffer cell C-type lectin receptor CLEC4F”. X-ray diffraction, 1 ligand (CA), 9 pockets (best druggability 0.82). MolNFT v1 #153599 on GenesisL1: 3D structure, binding…
- PDB
- 6JJJ
- Type
- protein
- Length
- 906 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-type lectin domain family 4 member F
- UniProt
- P70194
- Ligands
- CA
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | C-type lectin domain family 4 member F | protein | 151 | 25% helix, 23% strand | P70194 |
Ligands and binding sites
- CA · Calcium ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.82 | 0.84 | 116 | empty |
| 2 | 1039 | 0.82 | 0.83 | 118 | empty |
| 3 | 524 | 0.75 | 0.83 | 58 | empty |
| 4 | 729 | 0.74 | 0.80 | 90 | empty |
| 5 | 438 | 0.60 | 0.75 | 37 | empty |
Interfaces
6 interfaces between chains.
- D–F · 929 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 913 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 889 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 685 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 677 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6JJJ · Trimeric structure of Kupffer cell C-type lectin receptor Clec4f · the same entry in another collection · chain F against F, TM-score 1.00
- P70194 · AlphaFold monomer V2.0 prediction for C-type lectin domain family 4 member F (P70194) · a predicted model of the same protein · chain E against A, TM-score 0.95
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 P70194
- Elsewhere: RCSB PDB 6JJJ · PDBe 6JJJ · UniProt P70194
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