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Crystal structure of acpa E4 in complex with cii-C-13-cit

Analyse Crystal structure of acpa E4 in complex with cii-C-13-cit in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5OCX
Type: protein
Length: 444 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab fragment anti-citrullinated protein antibody E4 - light chain; Fab fragment of…
Ligands: CIR
Pockets: 2 · best druggability 0.59

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab fragment anti-citrullinated protein antibody E4 - light chain	protein	217	9% helix, 50% strand	—
H	Fab fragment of anti-citrullinated protein antibody E4 - heavy chain	protein	218	4% helix, 53% strand	—
A	Cii-C-13-cit	protein	9	33% helix, 0% strand	—

Ligands and binding sites

CIR · Citrulline · ligand · chains L, H, A
EDO · 1,2-ethanediol · additive · chains L, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	463	0.59	0.75	49	empty
2	110	0.40	0.76	19	empty

Interfaces

3 interfaces between chains.

L–H · 1895 Å² buried · 17 hydrogen bonds · protein-protein
H–A · 327 Å² buried · 4 hydrogen bonds · protein-protein
L–A · 208 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 5 disulfide, 2 covalent, 1 modified (disulfide, covalent ligand, cyclization).

Compared structures

5OCX · Crystal structure of ACPA E4 in complex with CII-C-13-CIT · 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 5OCX · PDBe 5OCX

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