Research workbench
Structure of anticalin N9B in complex with extra-domain B of human oncofetal fibronectin
Analyse Structure of anticalin N9B in complex with extra-domain B of human oncofetal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N48
- Type
- protein
- Length
- 534 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin; Fibronectin
- UniProt
- P80188, P02751
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neutrophil gelatinase-associated lipocalin | protein | 175 | 13% helix, 42% strand | P80188 |
| B | Fibronectin | protein | 92 | 0% helix, 51% strand | P02751 |
| C | Neutrophil gelatinase-associated lipocalin | protein | 174 | 13% helix, 42% strand | P80188 |
| D | Fibronectin | protein | 93 | 0% helix, 51% strand | P02751 |
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.83 | 0.84 | 127 | empty |
| 2 | 261 | 0.72 | 0.86 | 42 | empty |
| 3 | 425 | 0.71 | 0.82 | 55 | empty |
| 4 | 90 | 0.32 | 0.73 | 20 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1146 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1128 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 300 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 279 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5N48 · Structure of Anticalin N9B in complex with extra-domain B of human oncofetal fibronectin · the same entry in another collection · chain A against A, TM-score 1.00
- P02751 · AlphaFold monomer V2.0 prediction for fibronectin (P02751) · a predicted model of the same protein · chain D against A, TM-score 0.93
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 P80188
- Every structure of UniProt P02751
- Elsewhere: RCSB PDB 5N48 · PDBe 5N48 · UniProt P80188 · UniProt P02751
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