MolNFT v1 · #137113 · protein

Crystal structure of a Fab binding to extracellular domain 5 of cadherin-6

5VEB · Anti-CDH6 Fab heavy chain: “Crystal structure of a Fab binding to extracellular domain 5 of cadherin-6”. X-ray diffraction, 1 ligand (A2G), 13 pockets (best druggability 0.63). MolNFT v1 #137113 on GenesisL1: 3D structure, binding…

PDB: 5VEB
Type: protein
Length: 1,084 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anti-CDH6 Fab heavy chain; Anti-CDH6 Fab light chain; Cadherin-6
UniProt: S6B291, P01834, P55285
Ligands: A2G
Pockets: 13 · best druggability 0.63

Structure

x-ray diffraction · 4 distinct chains · 4% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, H	Anti-CDH6 Fab heavy chain	protein	221	7% helix, 52% strand	S6B291
B, L	Anti-CDH6 Fab light chain	protein	215	6% helix, 53% strand	P01834
X	Cadherin-6	protein	105	0% helix, 49% strand	P55285
Y	Cadherin-6	protein	107	0% helix, 49% strand	P55285

Ligands and binding sites

A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 4 copies · chains B, X, L, Y
SIN · Succinic acid · additive · chains A, B, X

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

Pockets

13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	580	0.63	0.74	66	empty
2	230	0.62	0.82	36	empty
3	598	0.61	0.74	62	empty
4	213	0.59	0.81	39	empty
5	152	0.58	0.83	28	empty

Interfaces

9 interfaces between chains.

H–L · 1977 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1935 Å² buried · 20 hydrogen bonds · protein-protein
L–Y · 734 Å² buried · 11 hydrogen bonds · protein-protein
B–X · 729 Å² buried · 10 hydrogen bonds · protein-protein
A–X · 653 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 4 glycan, 1 covalent (disulfide, O-glycosylation, additive adduct).

Compared structures

5VEB · Crystal structure of a Fab binding to extracellular domain 5 of Cadherin-6 · the same entry in another collection · chain Y against Y, TM-score 1.00
P55285 · AlphaFold monomer V2.0 prediction for cadherin-6 (P55285) · a predicted model of the same protein · chain X against A, TM-score 0.86
P01834 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01834) · a predicted model of the same protein · chain B against A, TM-score 0.49

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt S6B291
Every structure of UniProt P01834
Every structure of UniProt P55285
Elsewhere: RCSB PDB 5VEB · PDBe 5VEB · UniProt S6B291 · UniProt P01834 · UniProt P55285

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.