MolNFT v1 · #115475 · protein
Complex structure of norrin with human frizzled 4
5CL1 · Maltose-binding periplasmic PROTEIN,NORRIN: “Complex structure of norrin with human frizzled 4”. X-ray diffraction, 1 ligand (NAG), 13 pockets (best druggability 0.78). MolNFT v1 #115475 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5CL1
- Type
- protein
- Length
- 1,177 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic PROTEIN,NORRIN; Frizzled-4
- UniProt
- P0AEY0, Q00604, Q9ULV1
- Ligands
- NAG
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose-binding periplasmic PROTEIN,NORRIN | protein | 472 | 36% helix, 26% strand | P0AEY0, Q00604 |
| B | Maltose-binding periplasmic PROTEIN,NORRIN | protein | 470 | 36% helix, 26% strand | P0AEY0, Q00604 |
| C | Frizzled-4 | protein | 117 | 39% helix, 9% strand | Q9ULV1 |
| D | Frizzled-4 | protein | 118 | 39% helix, 7% strand | Q9ULV1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.78 | 0.80 | 73 | empty |
| 2 | 760 | 0.72 | 0.77 | 58 | empty |
| 3 | 303 | 0.65 | 0.81 | 39 | empty |
| 4 | 277 | 0.62 | 0.79 | 30 | empty |
| 5 | 347 | 0.61 | 0.78 | 49 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1698 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1559 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1130 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide (disulfide).
Compared structures
- 5CL1 · Complex structure of Norrin with human Frizzled 4 · the same entry in another collection · chain D against D, TM-score 1.00
- Q9ULV1 · AlphaFold monomer V2.0 prediction for frizzled-4 (Q9ULV1) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q00604 · AlphaFold monomer V2.0 prediction for norrin (Q00604) · a predicted model of the same protein · chain A against A, TM-score 0.25
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 P0AEY0
- Every structure of UniProt Q00604
- Every structure of UniProt Q9ULV1
- Elsewhere: RCSB PDB 5CL1 · PDBe 5CL1 · UniProt P0AEY0 · UniProt Q00604 · UniProt Q9ULV1
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