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Structure of catalytic elimination antibody 13G5 from a crystal in space group P2(1)

Analyse Structure of catalytic elimination antibody 13G5 from a crystal in space group… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2GJZ
Type: protein
Length: 876 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catalytic elimination antibody 13G5 light chain; Catalytic elimination antibody 13G5…
Ligands: ZN
Pockets: 9 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, A	Catalytic elimination antibody 13G5 light chain	protein	217	6% helix, 52% strand	—
H, B	Catalytic elimination antibody 13G5 heavy chain	protein	221	4% helix, 51% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 11 copies · chains L, H, A, B

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

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	299	0.59	0.78	45	empty
2	386	0.57	0.75	53	empty
3	113	0.57	0.84	22	ZN
4	377	0.56	0.74	47	empty
5	51	0.55	0.90	19	ZN

Interfaces

3 interfaces between chains.

L–H · 1841 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1774 Å² buried · 14 hydrogen bonds · protein-protein
H–A · 62 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

2GJZ · Structure of Catalytic Elimination Antibody 13G5 from a crystal in space group P2(1) · 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 2GJZ · PDBe 2GJZ

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