MolNFT v1 · #163171 · protein
Structure of the scin stabilized C3BBB convertase bound to properdin
6RUR: “Structure of the scin stabilized C3BBB convertase bound to properdin”. X-ray diffraction, 5 ligands (NAG, MAN, FUC), 20 pockets (best druggability 0.80). MolNFT v1 #163171 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6RUR
- Type
- protein
- Length
- 4,926 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Properdin; Complement C3; Complement factor B; Inhibitor
- EC
- 3.4.21.47
- UniProt
- P27918, P01024, P00751, A0A0H2DUF0
- Ligands
- NAG, MAN, FUC, BGC, MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| U, X | Properdin | protein | 106 | 4% helix, 38% strand | P27918 |
| V, Y | Properdin | protein | 210 | 0% helix, 36% strand | P27918 |
| A, G | Complement C3 | protein | 645 | 7% helix, 51% strand | P01024 |
| B, H | Complement C3 | protein | 913 | 25% helix, 31% strand | P01024 |
| J, L | Complement factor B (EC 3.4.21.47) | protein | 505 | 25% helix, 26% strand | P00751 |
| N, Q | Inhibitor | protein | 84 | 87% helix, 0% strand | A0A0H2DUF0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains V, Y, A, B, G, H, J, L
- MAN · alpha-D-mannopyranose · sugar · 18 copies · chains U, V, X, Y
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains U, V, X, Y
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains U, V, X, Y
- MG · Magnesium ion · metal · 2 copies · chains B, L, H, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1193 | 0.80 | 0.82 | 88 | empty |
| 2 | 1166 | 0.79 | 0.81 | 92 | empty |
| 3 | 505 | 0.78 | 0.85 | 60 | empty |
| 4 | 953 | 0.76 | 0.79 | 75 | empty |
| 5 | 507 | 0.75 | 0.83 | 44 | empty |
Interfaces
25 interfaces between chains.
- A–B · 5309 Ų buried · 79 hydrogen bonds · protein-protein
- G–H · 5268 Ų buried · 80 hydrogen bonds · protein-protein
- A–G · 1492 Ų buried · 10 hydrogen bonds · protein-protein
- X–Y · 1222 Ų buried · 9 hydrogen bonds · protein-protein
- U–V · 1211 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 disulfide, 32 glycan (disulfide, C-mannosylation, N-glycosylation, O-glycosylation).
Compared structures
- 6RUR · Structure of the SCIN stabilized C3bBb convertase bound to properdin · the same entry in another collection · chain Q against Q, 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 P27918
- Every structure of UniProt P01024
- Every structure of UniProt P00751
- Every structure of UniProt A0A0H2DUF0
- Elsewhere: RCSB PDB 6RUR · PDBe 6RUR · UniProt P27918 · UniProt P01024 · UniProt P00751 · UniProt A0A0H2DUF0
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