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Crystal structure of Fab dx-2930

Analyse Crystal structure of Fab dx-2930 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4PUB
Type: protein
Length: 424 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dx-2930 heavy chain; Dx-2930 light chain
Ligands: CL
Pockets: 5 · best druggability 0.53

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Dx-2930 heavy chain	protein	212	8% helix, 53% strand	—
L	Dx-2930 light chain	protein	212	6% helix, 51% strand	—

Ligands and binding sites

CL · Chloride ion · ion · chains H, L

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	337	0.53	0.74	42	empty
2	64	0.31	0.75	22	empty
3	77	0.31	0.73	17	empty
4	70	0.29	0.73	15	CL
5	51	0.24	0.73	14	empty

Interfaces

1 interface between chains.

H–L · 1826 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4PUB · Crystal structure of Fab DX-2930 · 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 4PUB · PDBe 4PUB

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