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Crystal structure of a murine antibody Fab 528

Analyse Crystal structure of a murine antibody Fab 528 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2Z4Q
Type: protein
Length: 437 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anti EGFR antibody Fab, light chain; Anti EGFR antibody Fab, heavy chain
Ligands: CD, CL
Pockets: 5 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Anti EGFR antibody Fab, light chain	protein	219	6% helix, 52% strand	—
B	Anti EGFR antibody Fab, heavy chain	protein	218	6% helix, 51% strand	—

Ligands and binding sites

CD · Cadmium ion · metal · 2 copies · chains A, B
CL · Chloride ion · ion · chains A

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

Pockets

5 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	680	0.64	0.74	66	empty
2	126	0.43	0.76	27	empty
3	98	0.38	0.75	23	empty
4	74	0.33	0.75	16	empty
5	77	0.30	0.73	19	empty

Interfaces

1 interface between chains.

A–B · 1923 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

2Z4Q · Crystal structure of a murine antibody FAB 528 · the same entry in another collection · chain A against A, 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 2Z4Q · PDBe 2Z4Q

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