MolNFT v1 · #173522 · protein
Cryo-EM structure of complement C4B in complex with nanobody E3
7B2M · Complement C4 beta chain: “Cryo-EM structure of complement C4B in complex with nanobody E3”. Electron microscopy, 1 ligand (NAG), 18 pockets (best druggability 0.73). MolNFT v1 #173522 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7B2M
- Type
- protein
- Length
- 1,506 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
- 18 · best druggability 0.73
Structure
electron microscopy · 4 distinct chains · 16% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C4 beta chain | protein | 650 | 7% helix, 45% strand | P0C0L4 |
| B | Complement C4 alpha chain | protein | 614 | 30% helix, 26% strand | P0C0L4 |
| C | Complement C4 gamma chain | protein | 130 | 7% helix, 41% strand | P0C0L4 |
| D | Anti-C4B nanobody E3 | protein | 112 | 5% helix, 41% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.73 | 0.89 | 39 | empty |
| 2 | 692 | 0.72 | 0.79 | 64 | empty |
| 3 | 624 | 0.67 | 0.76 | 51 | empty |
| 4 | 238 | 0.64 | 0.82 | 47 | empty |
| 5 | 283 | 0.63 | 0.81 | 39 | empty |
Interfaces
5 interfaces between chains.
- A–B · 5160 Ų buried · 86 hydrogen bonds · protein-protein
- B–C · 2495 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 845 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 773 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 116 Ų buried · 1 hydrogen bond · 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 7B2M · PDBe 7B2M · UniProt P0C0L4
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