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Crystal structure of DC8E8 Fab at pH 7.0 containing a zn atom

Analyse Crystal structure of DC8E8 Fab at pH 7.0 containing a zn atom in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MUQ
Type: protein
Length: 878 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antibody Fab heavy chain; Antibody kappa light chain
Ligands: ZN
Pockets: 15 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, A	Antibody Fab heavy chain	protein	220	9% helix, 52% strand	—
L, B	Antibody kappa light chain	protein	219	7% helix, 53% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains L, B
IMD · Imidazole · additive · 2 copies · chains L, B

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

Pockets

15 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	405	0.56	0.74	54	empty
2	285	0.52	0.75	39	empty
3	252	0.51	0.75	38	empty
4	240	0.49	0.74	32	empty
5	70	0.48	0.84	22	empty

Interfaces

3 interfaces between chains.

H–L · 1875 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1874 Å² buried · 17 hydrogen bonds · protein-protein
H–A · 490 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 modified (disulfide, cyclization).

Compared structures

5MUQ · Crystal structure of DC8E8 Fab at pH 7.0 containing a Zn atom · the same entry in another collection · chain H against H, 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 5MUQ · PDBe 5MUQ

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