Research workbench
Crystal structure of mouse pedf in complex with heterotrimeric collagen model peptide.
Analyse Crystal structure of mouse pedf in complex with heterotrimeric collagen model… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LOS
- Type
- protein
- Length
- 447 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pigment epithelium-derived factor; Collagen model peptide, type I, alpha 2; Collagen…
- UniProt
- P97298
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pigment epithelium-derived factor | protein | 369 | 33% helix, 32% strand | P97298 |
| F | Collagen model peptide, type I, alpha 2 | protein | 26 | 0% helix, 0% strand | — |
| G | Collagen model peptide, type I, alpha 1 | protein | 27 | 0% helix, 0% strand | — |
| H | Collagen model peptide, type I, alpha 1 | protein | 25 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.59 | 0.76 | 39 | empty |
| 2 | 109 | 0.47 | 0.79 | 24 | empty |
| 3 | 54 | 0.36 | 0.79 | 21 | empty |
Interfaces
6 interfaces between chains.
- G–H · 919 Ų buried · 11 hydrogen bonds · protein-protein
- F–H · 867 Ų buried · 11 hydrogen bonds · protein-protein
- F–G · 845 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 596 Ų buried · 1 hydrogen bond · protein-protein
- A–G · 330 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (hydroxylation).
Compared structures
- 6LOS · Crystal structure of mouse PEDF in complex with heterotrimeric collagen model peptide. · the same entry in another collection · chain A against A, TM-score 1.00
- P97298 · AlphaFold monomer V2.0 prediction for pigment epithelium-derived factor (P97298) · a predicted model of the same protein · 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 P97298
- Elsewhere: RCSB PDB 6LOS · PDBe 6LOS · UniProt P97298
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