Research workbench

Coltuximab Fab in complex with anti-kappa vhh domain

Analyse Coltuximab Fab in complex with anti-kappa vhh domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ANI
Type: protein
Length: 1,088 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anti-kappa vhh domain; Coltuximab Fab heavy chain; Coltuximab Fab light chain
Pockets: 13 · best druggability 0.77

Structure

x-ray diffraction · 6 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Anti-kappa vhh domain	protein	119	3% helix, 49% strand	—
K	Anti-kappa vhh domain	protein	120	5% helix, 48% strand	—
H	Coltuximab Fab heavy chain	protein	216	9% helix, 52% strand	—
L	Coltuximab Fab light chain	protein	210	5% helix, 50% strand	—
I	Coltuximab Fab heavy chain	protein	214	10% helix, 51% strand	—
M	Coltuximab Fab light chain	protein	209	6% helix, 49% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains H, I, M, L

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

Pockets

13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	573	0.77	0.84	91	empty
2	793	0.77	0.81	93	GOL
3	586	0.77	0.84	86	empty
4	112	0.58	0.86	33	empty
5	108	0.57	0.85	34	empty

Interfaces

6 interfaces between chains.

H–L · 1804 Å² buried · 15 hydrogen bonds · protein-protein
I–M · 1730 Å² buried · 16 hydrogen bonds · protein-protein
A–M · 568 Å² buried · 3 hydrogen bonds · protein-protein
K–L · 552 Å² buried · 5 hydrogen bonds · protein-protein
H–I · 342 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6ANI · Coltuximab Fab in complex with anti-Kappa VHH domain · 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 6ANI · PDBe 6ANI

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