MolNFT v1 · #155962 · protein
Crystal structure of mouse pedf in complex with heterotrimeric collagen model peptide.
6LOS · Pigment epithelium-derived factor: “Crystal structure of mouse pedf in complex with heterotrimeric collagen model peptide.”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.59). MolNFT v1 #155962 on GenesisL1: 3D…
- 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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