MolNFT v1 · #73400 · protein
The crystal structure of the putative lipoprotein from colwellia psychrerythraea
3O0Y: “The crystal structure of the putative lipoprotein from colwellia psychrerythraea”. X-ray diffraction, 1 ligand (SO4), 17 pockets (best druggability 0.88). MolNFT v1 #73400 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3O0Y
- Type
- protein
- Length
- 1,755 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoprotein
- UniProt
- Q47Z72
- Ligands
- SO4
- Pockets
- 17 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipoprotein | protein | 585 | 67% helix, 3% strand | Q47Z72 |
| B, C | Lipoprotein | protein | 585 | 66% helix, 3% strand | Q47Z72 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C
- GOL · Glycerol · additive · 8 copies · chains A, B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.88 | 0.89 | 100 | SO4 |
| 2 | 979 | 0.87 | 0.89 | 94 | SO4 |
| 3 | 1164 | 0.85 | 0.86 | 103 | SO4, GOL |
| 4 | 808 | 0.82 | 0.85 | 92 | GOL |
| 5 | 366 | 0.74 | 0.85 | 48 | TRS |
Interfaces
3 interfaces between chains.
- A–B · 704 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 646 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 624 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3O0Y · The crystal structure of the putative lipoprotein from Colwellia psychrerythraea · 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 Q47Z72
- Elsewhere: RCSB PDB 3O0Y · PDBe 3O0Y · UniProt Q47Z72
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