Research workbench
Human complement component C3B in complex with apl-1030
Analyse Human complement component C3B in complex with apl-1030 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TV9
- Type
- protein
- Length
- 1,601 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3 beta chain; Complement C3B alpha' chain; Apl-1030 nanofitin
- UniProt
- P01024
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C3 beta chain | protein | 636 | 6% helix, 46% strand | P01024 |
| B | Complement C3B alpha' chain | protein | 902 | 23% helix, 26% strand | P01024 |
| C | Apl-1030 nanofitin | protein | 63 | 27% helix, 40% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.77 | 0.79 | 85 | empty |
| 2 | 55 | 0.72 | 0.98 | 20 | empty |
| 3 | 459 | 0.72 | 0.82 | 45 | empty |
| 4 | 564 | 0.68 | 0.78 | 72 | empty |
| 5 | 198 | 0.57 | 0.80 | 29 | empty |
Interfaces
2 interfaces between chains.
- A–B · 5060 Ų buried · 62 hydrogen bonds · protein-protein
- A–C · 1194 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 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 P01024
- Elsewhere: RCSB PDB 7TV9 · PDBe 7TV9 · UniProt P01024
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