MolNFT v1 · #171083 · protein
The HC4NB8 complement inhibitory nanobody in complex with C4B
6YSQ · Complement C4 beta chain: “The HC4NB8 complement inhibitory nanobody in complex with C4B”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.80). MolNFT v1 #171083 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6YSQ
- Type
- protein
- Length
- 3,372 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C4 beta chain; Complement C4-a alpha chain; Complement C4 gamma chain; HC4NB8…
- UniProt
- P0C0L4, P0C0L5
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Complement C4 beta chain | protein | 651 | 7% helix, 48% strand | P0C0L4 |
| C | Complement C4-a alpha chain | protein | 633 | 27% helix, 27% strand | P0C0L4 |
| E, F | Complement C4 gamma chain | protein | 277 | 12% helix, 37% strand | P0C0L5 |
| D | Complement C4-a alpha chain | protein | 635 | 28% helix, 26% strand | P0C0L4 |
| G, H | HC4NB8 nanobody | protein | 124 | 2% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C, B, D
- BMA · beta-D-mannopyranose · sugar · 4 copies
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 | 583 | 0.80 | 0.85 | 62 | empty |
| 2 | 968 | 0.75 | 0.78 | 70 | empty |
| 3 | 844 | 0.72 | 0.77 | 64 | empty |
| 4 | 186 | 0.69 | 0.87 | 30 | empty |
| 5 | 700 | 0.69 | 0.77 | 60 | empty |
Interfaces
17 interfaces between chains.
- A–C · 5362 Ų buried · 77 hydrogen bonds · protein-protein
- B–D · 5275 Ų buried · 82 hydrogen bonds · protein-protein
- C–E · 2702 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 2691 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 888 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
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 P0C0L4
- Every structure of UniProt P0C0L5
- Elsewhere: RCSB PDB 6YSQ · PDBe 6YSQ · UniProt P0C0L4 · UniProt P0C0L5
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