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High-resolution structure of blue fluorescent antibody EP2-19G2 in complex with stilbene hapten at 100K

Analyse High-resolution structure of blue fluorescent antibody EP2-19G2 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3CFB
Type: protein
Length: 862 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Blue fluorescent antibody EP2-19G2-kappa light chain; Blue fluorescent antibody…
Ligands: SPB
Pockets: 14 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, A	Blue fluorescent antibody EP2-19G2-kappa light chain	protein	218	6% helix, 48% strand	—
H, B	Blue fluorescent antibody EP2-19G2-IGG2B heavy chain	protein	213	6% helix, 50% strand	—

Ligands and binding sites

SPB · 4-(4-styryl-phenylcarbamoyl)-butyric acid · ligand · 2 copies · chains L, H, A, B
GOL · Glycerol · additive · 6 copies · chains L, H, A, B

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

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	119	0.73	0.93	23	SPB
2	123	0.72	0.92	24	SPB
3	487	0.71	0.81	59	empty
4	681	0.66	0.75	64	empty
5	499	0.61	0.75	63	empty

Interfaces

5 interfaces between chains.

A–B · 1819 Å² buried · 17 hydrogen bonds · protein-protein
L–H · 1746 Å² buried · 16 hydrogen bonds · protein-protein
H–B · 411 Å² buried · 12 hydrogen bonds · protein-protein
H–A · 186 Å² buried · 1 hydrogen bond · protein-protein
L–B · 132 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

3CFB · High-resolution structure of blue fluorescent antibody EP2-19G2 in complex with stilbene… · the same entry in another collection · chain L against L, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 3CFB · PDBe 3CFB

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