Research workbench

Fab fragment of calcium-dependent antigen binding antibody, 6RL#9

Analyse Fab fragment of calcium-dependent antigen binding antibody, 6RL#9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5AZE
Type: protein
Length: 430 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 6RL#9 Fab light chain; 6RL#9 Fab heavy chain
Ligands: CA
Pockets: 4 · best druggability 0.55

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	6RL#9 Fab light chain	protein	206	7% helix, 51% strand	—
H	6RL#9 Fab heavy chain	protein	224	8% helix, 52% strand	—

Ligands and binding sites

CA · Calcium ion · metal · chains 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	384	0.55	0.74	62	empty
2	142	0.43	0.75	23	empty
3	134	0.41	0.75	21	empty
4	50	0.28	0.75	18	empty

Interfaces

1 interface between chains.

L–H · 1799 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 1 modified (disulfide, cyclization).

Compared structures

5AZE · Fab fragment of calcium-dependent antigen binding antibody, 6RL#9 · 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 5AZE · PDBe 5AZE

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