Research workbench
Structure of the scin stabilized C3BBB convertase bound to properdin and a the non-inhibitory nanobody HFPNB1
Analyse Structure of the scin stabilized C3BBB convertase bound to properdin and a the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RUV
- Type
- protein
- Length
- 5,240 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody HFPNB1; Properdin; Complement C3; Complement factor B; Inhibitor
- EC
- 3.4.21.47
- UniProt
- P27918, P01024, P00751, A0A0H2DUF0
- Ligands
- MAN, NAG, FUC, BGC, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R, S | Nanobody HFPNB1 | protein | 124 | 5% helix, 51% strand | — |
| U | Properdin | protein | 105 | 4% helix, 41% strand | P27918 |
| V, Y | Properdin | protein | 215 | 2% helix, 33% strand | P27918 |
| X | Properdin | protein | 163 | 2% helix, 34% strand | P27918 |
| A, G | Complement C3 | protein | 645 | 7% helix, 49% 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, 25% strand | P00751 |
| N, Q | Inhibitor | protein | 84 | 86% helix, 0% strand | A0A0H2DUF0 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 21 copies · chains U, V, X, Y
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains V, Y, A, B, G, H, J, L
- FUC · alpha-L-fucopyranose · sugar · 7 copies · chains U, V, X, R, Y
- BGC · beta-D-glucopyranose · sugar · 5 copies · chains U, S, V, X, R, Y
- MG · Magnesium ion · metal · 2 copies · chains H, J, B, L
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 | 1133 | 0.81 | 0.83 | 107 | empty |
| 2 | 128 | 0.78 | 0.96 | 33 | empty |
| 3 | 964 | 0.78 | 0.80 | 80 | empty |
| 4 | 429 | 0.76 | 0.86 | 64 | empty |
| 5 | 1152 | 0.75 | 0.78 | 85 | empty |
Interfaces
30 interfaces between chains.
- A–B · 5373 Ų buried · 91 hydrogen bonds · protein-protein
- G–H · 5322 Ų buried · 84 hydrogen bonds · protein-protein
- A–G · 1471 Ų buried · 7 hydrogen bonds · protein-protein
- X–Y · 1308 Ų buried · 10 hydrogen bonds · protein-protein
- U–V · 1285 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 65 disulfide, 36 glycan (disulfide, C-mannosylation, N-glycosylation, O-glycosylation).
Compared structures
- 6RUV · Structure of the SCIN stabilized C3bBb convertase bound to Properdin and a the… · 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 6RUV · PDBe 6RUV · UniProt P27918 · UniProt P01024 · UniProt P00751 · UniProt A0A0H2DUF0
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