MolNFT v1 · #113007 · protein

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

5A2K · Ig lambda-1 chain V region S43: “Crystal structure of scfv-SM3 in complex with apd-tgalnac-rp”. X-ray diffraction, 1 ligand (A2G), 3 pockets (best druggability 0.31). MolNFT v1 #113007 on GenesisL1: 3D structure, binding sites and…

PDB: 5A2K
Type: protein
Length: 231 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ig lambda-1 chain V region S43; Antigen tn, thr is covalently bound to galnac
UniProt: P01801, P01727
Ligands: A2G
Pockets: 3 · best druggability 0.31

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Ig lambda-1 chain V region S43	protein	225	8% helix, 53% strand	P01801, P01727
P	Antigen tn, thr is covalently bound to galnac	protein	6	0% helix, 0% strand	—

Ligands and binding sites

A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · chains H, P
EDO · 1,2-ethanediol · additive · 6 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	72	0.31	0.74	15	empty
2	70	0.31	0.74	22	empty
3	50	0.28	0.76	15	EDO

Interfaces

1 interface between chains.

H–P · 409 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide, 1 glycan (disulfide, O-glycosylation).

Compared structures

5A2K · Crystal structure of scFv-SM3 in complex with APD-TGalNAc-RP · the same entry in another collection · chain H against H, TM-score 1.00
P01801 · AlphaFold monomer V2.0 prediction for ig heavy chain V-III region J606 (P01801) · a predicted model of the same protein · chain H against A, TM-score 0.50
P01727 · AlphaFold monomer V2.0 prediction for ig lambda-1 chain V region S43 (P01727) · a predicted model of the same protein · chain H against A, TM-score 0.48

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 P01801
Every structure of UniProt P01727
Elsewhere: RCSB PDB 5A2K · PDBe 5A2K · UniProt P01801 · UniProt P01727

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