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Crystal structure of vhh-based Fab-fragment of antibody bcd-085

Analyse Crystal structure of vhh-based Fab-fragment of antibody bcd-085 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6QKD
Type: protein
Length: 1,742 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab heavy chain; Fab light chain
Ligands: SO4, CL
Pockets: 19 · best druggability 0.78

Structure

x-ray diffraction · 6 distinct chains · 8% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab heavy chain	protein	222	8% helix, 48% strand	—
I	Fab heavy chain	protein	221	10% helix, 49% strand	—
J	Fab heavy chain	protein	223	7% helix, 51% strand	—
K	Fab heavy chain	protein	223	10% helix, 48% strand	—
L, O, T	Fab light chain	protein	213	7% helix, 50% strand	—
M	Fab light chain	protein	214	7% helix, 50% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 10 copies · chains H, I, K, L, J, M, O, T
CL · Chloride ion · ion · 3 copies · chains I, K, T

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

Pockets

19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1057	0.78	0.80	92	empty
2	843	0.76	0.80	74	empty
3	1063	0.76	0.79	117	empty
4	589	0.72	0.80	71	empty
5	555	0.69	0.78	50	empty

Interfaces

13 interfaces between chains.

H–L · 1077 Å² buried · 5 hydrogen bonds · protein-protein
K–O · 973 Å² buried · 5 hydrogen bonds · protein-protein
J–M · 968 Å² buried · 4 hydrogen bonds · protein-protein
I–T · 862 Å² buried · 6 hydrogen bonds · protein-protein
I–L · 823 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

6QKD · CRYSTAL STRUCTURE OF vhh-based FAB-fragment of antibody BCD-085 · 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 6QKD · PDBe 6QKD

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