MolNFT v1 · #74187 · protein
Crystal structure of the domain V from BETA2-glycoprotein I
3OP8 · Beta-2-glycoprotein 1: “Crystal structure of the domain V from BETA2-glycoprotein I”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.52). MolNFT v1 #74187 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3OP8
- Type
- protein
- Length
- 170 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-2-glycoprotein 1
- UniProt
- P02749
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-2-glycoprotein 1 | protein | 85 | 8% helix, 36% strand | P02749 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.52 | 0.82 | 22 | SO4 |
| 2 | 101 | 0.51 | 0.82 | 26 | empty |
| 3 | 111 | 0.49 | 0.81 | 22 | SO4 |
| 4 | 58 | 0.27 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 335 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
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 P02749
- Elsewhere: RCSB PDB 3OP8 · PDBe 3OP8 · UniProt P02749
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