MolNFT v1 · #151860 · protein

Crystal structure of epcam in complex with scfv

6I07 · Single chain fv: “Crystal structure of epcam in complex with scfv”. X-ray diffraction, 16 pockets (best druggability 0.79). MolNFT v1 #151860 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6I07
Type: protein
Length: 906 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Single chain fv; Epithelial cell adhesion molecule
UniProt: P16422
Pockets: 16 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 11% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Single chain fv	protein	228	4% helix, 51% strand	—
B	Single chain fv	protein	226	4% helix, 47% strand	—
C	Epithelial cell adhesion molecule	protein	225	19% helix, 25% strand	P16422
D	Epithelial cell adhesion molecule	protein	227	18% helix, 25% strand	P16422

Ligands and binding sites

GOL · Glycerol · additive · chains A

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

Pockets

16 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1074	0.79	0.80	88	empty
2	200	0.53	0.78	32	empty
3	106	0.50	0.81	18	empty
4	171	0.50	0.77	22	empty
5	148	0.47	0.77	20	empty

Interfaces

3 interfaces between chains.

C–D · 1339 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 943 Å² buried · 21 hydrogen bonds · protein-protein
B–D · 880 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide, 2 modified (disulfide, cyclization).

Compared structures

6I07 · Crystal structure of EpCAM in complex with scFv · the same entry in another collection · chain A against A, TM-score 1.00
P16422 · AlphaFold monomer V2.0 prediction for epithelial cell adhesion molecule (P16422) · a predicted model of the same protein · chain D against A, TM-score 0.96

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 P16422
Elsewhere: RCSB PDB 6I07 · PDBe 6I07 · UniProt P16422

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