MolNFT v1 · #20898 · protein
Crystal structure analysis of the bb segment of factor B complexed with 4-guanidinobenzoic acid
1RTK · Complement factor B bb fragment: “Crystal structure analysis of the bb segment of factor B complexed with 4-guanidinobenzoic acid”. X-ray diffraction, 4 ligands (GBS, NA, MG), 4 pockets (best druggability 0.55). MolNFT v1 #20898 on…
- PDB
- 1RTK
- Type
- protein
- Length
- 486 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement factor B bb fragment
- UniProt
- P00751
- Ligands
- GBS, NA, MG, IOD
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement factor B bb fragment | protein | 486 | 29% helix, 26% strand | P00751 |
Ligands and binding sites
- GBS · 4-guanidinobenzoic acid · 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
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.55 | 0.79 | 26 | empty |
| 2 | 169 | 0.52 | 0.79 | 38 | empty |
| 3 | 198 | 0.51 | 0.77 | 22 | GBS |
| 4 | 70 | 0.48 | 0.84 | 17 | empty |
Modifications
Observed in the structure: 6 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 1RTK · 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 1RTK · PDBe 1RTK · UniProt P00751
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