Research workbench
Cryo-EM structure of complement C4B in complex with nanobody B12
Analyse Cryo-EM structure of complement C4B in complex with nanobody B12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B2Q
- Type
- protein
- Length
- 1,495 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C4 beta chain; Complement C4 alpha chain; Complement C4 gamma chain; Anti-C4B…
- UniProt
- P0C0L4
- Ligands
- NAG
- Pockets
- 14 · best druggability 0.70
Structure
electron microscopy · 4 distinct chains · 16% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C4 beta chain | protein | 650 | 7% helix, 42% strand | P0C0L4 |
| B | Complement C4 alpha chain | protein | 600 | 31% helix, 21% strand | P0C0L4 |
| C | Complement C4 gamma chain | protein | 129 | 7% helix, 35% strand | P0C0L4 |
| D | Anti-C4B nanobody B12 | protein | 116 | 5% helix, 39% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.70 | 0.76 | 75 | empty |
| 2 | 565 | 0.70 | 0.79 | 65 | empty |
| 3 | 196 | 0.70 | 0.87 | 32 | empty |
| 4 | 259 | 0.65 | 0.82 | 41 | empty |
| 5 | 286 | 0.58 | 0.77 | 42 | empty |
Interfaces
5 interfaces between chains.
- A–B · 5150 Ų buried · 79 hydrogen bonds · protein-protein
- B–C · 2319 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 829 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 659 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 85 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 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
- Elsewhere: RCSB PDB 7B2Q · PDBe 7B2Q · UniProt P0C0L4
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