MolNFT v1 · #34039 · protein
Trivalent recognition unit of innate immunity system; crystal structure of human M-ficolin fibrinogen-like domain
2D39 · Ficolin-1: “Trivalent recognition unit of innate immunity system; crystal structure of human M-ficolin fibrinogen-like…”. X-ray diffraction, 1 ligand (CA), 10 pockets (best druggability 0.82). MolNFT v1 #34039 on GenesisL1: 3D…
- PDB
- 2D39
- Type
- protein
- Length
- 621 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ficolin-1
- UniProt
- O00602
- Ligands
- CA
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ficolin-1 | protein | 209 | 15% helix, 32% strand | O00602 |
| B | Ficolin-1 | protein | 200 | 15% helix, 33% strand | O00602 |
| C | Ficolin-1 | protein | 212 | 14% helix, 34% strand | O00602 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1143 | 0.82 | 0.83 | 120 | empty |
| 2 | 356 | 0.63 | 0.78 | 29 | empty |
| 3 | 156 | 0.58 | 0.82 | 27 | empty |
| 4 | 149 | 0.52 | 0.80 | 25 | empty |
| 5 | 74 | 0.46 | 0.82 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 554 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 545 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 526 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2D39 · Trivalent Recognition Unit of Innate Immunity System; Crystal Structure of human… · the same entry in another collection · chain A against A, TM-score 1.00
- O00602 · AlphaFold monomer V2.0 prediction for ficolin-1 (O00602) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 O00602
- Elsewhere: RCSB PDB 2D39 · PDBe 2D39 · UniProt O00602
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