MolNFT v1 · #119477 · protein

Crystal structure of glycopeptide 22 in complex with scfv-SM3

5FXC: “Crystal structure of glycopeptide 22 in complex with scfv-SM3”. X-ray diffraction, 3 pockets (best druggability 0.33). MolNFT v1 #119477 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5FXC
Type: protein
Length: 230 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Scfv-SM3; Glycopeptide
Pockets: 3 · best druggability 0.33

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Scfv-SM3	protein	224	9% helix, 52% strand	—
P	Glycopeptide	protein	6	0% helix, 0% strand	—

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 4 copies · chains H, P

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	83	0.33	0.74	24	empty
2	64	0.30	0.74	17	EDO
3	57	0.29	0.75	16	EDO

Interfaces

1 interface between chains.

H–P · 409 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5FXC · Crystal structure of glycopeptide 22 in complex with scFv-SM3 · 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 5FXC · PDBe 5FXC

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