Research workbench
Crystal structure analysis of the bb segment of factor B complexed with di-isopropyl-phosphate (dip)
Analyse Crystal structure analysis of the bb segment of factor B complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RS0
- Type
- protein
- Length
- 480 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement factor B
- EC
- 3.4.21.47
- UniProt
- P00751
- Ligands
- DFP, NA, MG, IOD
- Pockets
- 5 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement factor B (EC 3.4.21.47) | protein | 480 | 28% helix, 26% strand | P00751 |
Ligands and binding sites
- DFP · Diisopropyl phosphonate · ligand · chains A
- NA · Sodium ion · metal · 7 copies · chains A
- MG · Magnesium ion · metal · chains A
- IOD · Iodide ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.53 | 0.79 | 38 | empty |
| 2 | 169 | 0.50 | 0.77 | 21 | empty |
| 3 | 162 | 0.48 | 0.77 | 25 | DFP |
| 4 | 53 | 0.39 | 0.81 | 15 | empty |
| 5 | 51 | 0.28 | 0.74 | 18 | empty |
Modifications
Observed in the structure: 6 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 1RS0 · Crystal Structure Analysis of the Bb segment of Factor B complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P00751 · AlphaFold monomer V2.0 prediction for complement factor B (P00751) · a predicted model of the same protein · chain A against A, TM-score 0.80
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 P00751
- Elsewhere: RCSB PDB 1RS0 · PDBe 1RS0 · UniProt P00751
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