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Structure of anti-C3D FAB(3D8B) in complex with C3D

Analyse Structure of anti-C3D FAB(3D8B) in complex with C3D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7UE9
Type: protein
Length: 744 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab light chain; Fab heavy chain; Complement C3DG fragment
UniProt: P01024
Pockets: 8 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab light chain	protein	219	6% helix, 50% strand	—
H	Fab heavy chain	protein	214	10% helix, 51% strand	—
C	Complement C3DG fragment	protein	311	63% helix, 2% strand	P01024

Ligands and binding sites

GOL · Glycerol · additive · 10 copies · chains L, H, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	440	0.63	0.77	48	GOL
2	326	0.60	0.78	39	empty
3	437	0.58	0.74	59	empty
4	192	0.48	0.76	25	empty
5	81	0.44	0.80	17	GOL

Interfaces

3 interfaces between chains.

L–H · 1671 Å² buried · 11 hydrogen bonds · protein-protein
L–C · 640 Å² buried · 11 hydrogen bonds · protein-protein
H–C · 600 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 1 modified (disulfide, cyclization).

Compared structures

7UE9 · Structure of anti-C3d Fab(3d8b) in complex with C3d · the same entry in another collection · chain L against L, TM-score 1.00
P01024 · AlphaFold monomer V2.0 prediction for complement C3 (P01024) · a predicted model of the same protein · chain C against A, TM-score 0.87

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 7UE9 · PDBe 7UE9 · UniProt P01024

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