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Crystal structure of Fab C2507

Analyse Crystal structure of Fab C2507 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3QPX
Type: protein
Length: 441 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab C2507 light chain; Fab C2507 heavy chain
Ligands: CD, SO4, CL
Pockets: 4 · best druggability 0.66

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab C2507 light chain	protein	213	5% helix, 51% strand	—
H	Fab C2507 heavy chain	protein	228	7% helix, 50% strand	—

Ligands and binding sites

CD · Cadmium ion · metal · 6 copies · chains L, H
SO4 · Sulfate ion · ion · 11 copies · chains L, H
CL · Chloride ion · ion · chains L
GOL · Glycerol · additive · 10 copies · chains L, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	732	0.66	0.75	69	GOL, SO4
2	52	0.51	0.88	18	GOL
3	97	0.37	0.75	18	GOL
4	62	0.30	0.75	13	empty

Interfaces

1 interface between chains.

L–H · 2041 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

3QPX · Crystal structure of Fab C2507 · 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 3QPX · PDBe 3QPX

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