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C3B in complex with a C3B specific Fab

Analyse C3B in complex with a C3B specific Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3G6J
Type: protein
Length: 3,960 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Complement C3 beta chain; Complement C3 alpha chain; Fab light chain; Fab heavy chain
UniProt: P01024
Ligands: CA
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 4 distinct chains · 15% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Complement C3 beta chain	protein	642	8% helix, 47% strand	P01024
B, D	Complement C3 alpha chain	protein	903	25% helix, 26% strand	P01024
E, G	Fab light chain	protein	214	6% helix, 51% strand	—
F, H	Fab heavy chain	protein	221	5% helix, 51% strand	—

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, C

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	908	0.86	0.88	93	empty
2	947	0.77	0.80	75	empty
3	728	0.75	0.80	55	empty
4	397	0.73	0.84	58	empty
5	425	0.73	0.83	41	empty

Interfaces

14 interfaces between chains.

A–B · 5172 Å² buried · 69 hydrogen bonds · protein-protein
C–D · 5029 Å² buried · 74 hydrogen bonds · protein-protein
E–F · 1974 Å² buried · 18 hydrogen bonds · protein-protein
G–H · 1930 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 1291 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 29 disulfide (disulfide).

Compared structures

3G6J · C3b in complex with a C3b specific Fab · the same entry in another collection · chain H against H, TM-score 1.00
P01024 · AlphaFold monomer V2.0 prediction for complement C3 (P01024) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 3G6J · PDBe 3G6J · UniProt P01024

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