Research workbench
Crystal structure of efb-C (N138A) / C3D complex
Analyse Crystal structure of efb-C (N138A) / C3D complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D5R
- Type
- protein
- Length
- 724 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3; Fibrinogen-binding protein
- UniProt
- P01024, A6QG59
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Complement C3 | protein | 297 | 64% helix, 2% strand | P01024 |
| C, D | Fibrinogen-binding protein | protein | 65 | 85% helix, 0% strand | A6QG59 |
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.84 | 0.97 | 45 | empty |
| 2 | 280 | 0.58 | 0.77 | 29 | empty |
| 3 | 293 | 0.57 | 0.77 | 34 | empty |
| 4 | 81 | 0.57 | 0.87 | 20 | empty |
| 5 | 259 | 0.56 | 0.77 | 29 | empty |
Interfaces
3 interfaces between chains.
- B–D · 906 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 899 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 659 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3D5R · Crystal Structure of Efb-C (N138A) / C3d Complex · the same entry in another collection · chain D against D, TM-score 1.00
- A6QG59 · AlphaFold monomer V2.0 prediction for fibrinogen-binding protein (A6QG59) · a predicted model of the same protein · chain C against A, TM-score 0.96
- P01024 · AlphaFold monomer V2.0 prediction for complement C3 (P01024) · a predicted model of the same protein · chain A against A, TM-score 0.90
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
- Every structure of UniProt A6QG59
- Elsewhere: RCSB PDB 3D5R · PDBe 3D5R · UniProt P01024 · UniProt A6QG59
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