Research workbench
Structural characterization of a novel monotreme-specific protein from the milk of the platypus
Analyse Structural characterization of a novel monotreme-specific protein from the milk… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B4M
- Type
- protein
- Length
- 687 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monotreme lactation protein
- UniProt
- A0A088CNJ7
- Ligands
- NAG, IOD
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Monotreme lactation protein | protein | 343 | 57% helix, 4% strand | A0A088CNJ7 |
| B | Monotreme lactation protein | protein | 344 | 57% helix, 4% strand | A0A088CNJ7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- IOD · Iodide ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.78 | 0.99 | 20 | empty |
| 2 | 68 | 0.75 | 0.98 | 18 | empty |
| 3 | 187 | 0.49 | 0.76 | 32 | empty |
| 4 | 113 | 0.44 | 0.78 | 14 | empty |
| 5 | 128 | 0.43 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 509 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6B4M · Structural characterization of a novel monotreme-specific protein from the milk of the… · 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 A0A088CNJ7
- Elsewhere: RCSB PDB 6B4M · PDBe 6B4M · UniProt A0A088CNJ7
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