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Crystal structure of scfv-SM3 in complex with apd-sethrgalnac-rp

Analyse Crystal structure of scfv-SM3 in complex with apd-sethrgalnac-rp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6FRJ
Type: protein
Length: 232 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Scfv-SM3; Apd-sethr-rp
Ligands: A2G, NH2
Pockets: 1 · best druggability 0.32

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Scfv-SM3	protein	226	8% helix, 52% strand	—
B	Apd-sethr-rp	protein	6	0% helix, 0% strand	—

Ligands and binding sites

A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · chains H, B
NH2 · Amino group · ion · chains H, B
EDO · 1,2-ethanediol · additive · 4 copies · chains H, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	85	0.32	0.73	18	empty

Interfaces

1 interface between chains.

H–B · 408 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide, 1 glycan, 1 modified (disulfide, glycosylation, nonstandard).

Compared structures

6FRJ · Crystal structure of scFv-SM3 in complex with APD-SeThrGalNAc-RP · 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 6FRJ · PDBe 6FRJ

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