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Structural characterization of the native fetuin-binding protein scilla campanulata agglutinin (scafet): a novel two-domain lectin
Analyse Structural characterization of the native fetuin-binding protein scilla… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DLP
- Type
- protein
- Length
- 1,358 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin scafet precursor
- UniProt
- Q9ZP48
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 0% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lectin scafet precursor | protein | 233 | 0% helix, 32% strand | Q9ZP48 |
| B | Lectin scafet precursor | protein | 221 | 0% helix, 24% strand | Q9ZP48 |
| C | Lectin scafet precursor | protein | 234 | 0% helix, 31% strand | Q9ZP48 |
| D | Lectin scafet precursor | protein | 223 | 0% helix, 34% strand | Q9ZP48 |
| E | Lectin scafet precursor | protein | 231 | 0% helix, 35% strand | Q9ZP48 |
| F | Lectin scafet precursor | protein | 216 | 0% helix, 27% strand | Q9ZP48 |
Pockets
17 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 832 | 0.79 | 0.82 | 77 | empty |
| 2 | 567 | 0.73 | 0.81 | 61 | empty |
| 3 | 503 | 0.72 | 0.81 | 56 | empty |
| 4 | 54 | 0.47 | 0.85 | 20 | empty |
| 5 | 122 | 0.46 | 0.79 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–C · 895 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 839 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 767 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 698 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 694 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 1DLP · Structural characterization of the native fetuin-binding protein scilla campanulata… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9ZP48
- Elsewhere: RCSB PDB 1DLP · PDBe 1DLP · UniProt Q9ZP48
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