MolNFT v1 · #183419 · protein
Structure of the nanobody stablized properdin bound alternative pathway proconvertase C3B:FB:FP
7NOZ · Complement C3 beta chain: “Structure of the nanobody stablized properdin bound alternative pathway proconvertase C3B:FB:FP”. X-ray diffraction, 6 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.85). MolNFT v1 #183419 on…
- PDB
- 7NOZ
- Type
- protein
- Length
- 2,754 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3 beta chain; Complement C3 alpha chain; Properdin; Complement factor B…
- EC
- 3.4.21.47
- UniProt
- P01024, P27918, P00751
- Ligands
- NAG, MAN, BMA, FUC, BGC, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 14% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C3 beta chain | protein | 642 | 7% helix, 50% strand | P01024 |
| B | Complement C3 alpha chain | protein | 906 | 24% helix, 31% strand | P01024 |
| C | Properdin | protein | 163 | 2% helix, 32% strand | P27918 |
| D | Properdin | protein | 207 | 0% helix, 32% strand | P27918 |
| F | Complement factor B (EC 3.4.21.47) | protein | 712 | 18% helix, 28% strand | P00751 |
| R | HFPNB1 nanobody | protein | 124 | 2% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B, D, F
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains C, D
- BMA · beta-D-mannopyranose · sugar · 5 copies
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains C, D, R
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains C, D, R
- MG · Magnesium ion · metal · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.85 | 0.86 | 77 | empty |
| 2 | 827 | 0.85 | 0.88 | 87 | empty |
| 3 | 951 | 0.85 | 0.86 | 83 | empty |
| 4 | 569 | 0.79 | 0.85 | 51 | empty |
| 5 | 439 | 0.76 | 0.85 | 42 | empty |
Interfaces
8 interfaces between chains.
- A–B · 5236 Ų buried · 62 hydrogen bonds · protein-protein
- B–F · 2828 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 1051 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 1022 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 705 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 41 disulfide, 15 glycan (disulfide, C-mannosylation, N-glycosylation, O-glycosylation).
Compared structures
- 7NOZ · Structure of the nanobody stablized properdin bound alternative pathway proconvertase… · the same entry in another collection · chain R against R, TM-score 1.00
- P01024 · AlphaFold monomer V2.0 prediction for complement C3 (P01024) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P27918 · AlphaFold monomer V2.0 prediction for properdin (P27918) · a predicted model of the same protein · chain D against A, TM-score 0.84
- P00751 · AlphaFold monomer V2.0 prediction for complement factor B (P00751) · a predicted model of the same protein · chain F against A, TM-score 0.57
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 P01024
- Every structure of UniProt P27918
- Every structure of UniProt P00751
- Elsewhere: RCSB PDB 7NOZ · PDBe 7NOZ · UniProt P01024 · UniProt P27918 · UniProt P00751
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