MolNFT v1 · #136877 · protein

Glycan binding protein Y3 from mushroom coprinus comatus possesses anti-leukemic activity

5V6J · Tmv resistance protein Y3: “Glycan binding protein Y3 from mushroom coprinus comatus possesses anti-leukemic activity”. X-ray diffraction, 3 pockets (best druggability 0.73). MolNFT v1 #136877 on GenesisL1: 3D structure, binding…

PDB: 5V6J
Type: protein
Length: 448 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tmv resistance protein Y3
UniProt: G3BK00
Pockets: 3 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Tmv resistance protein Y3	protein	112	26% helix, 31% strand	G3BK00

Ligands and binding sites

NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	507	0.73	0.82	52	NHE
2	223	0.56	0.79	33	empty
3	211	0.54	0.79	37	empty

Interfaces

4 interfaces between chains.

C–D · 1174 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 1133 Å² buried · 31 hydrogen bonds · protein-protein
B–C · 276 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 82 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 4 modified (disulfide, cyclization).

Compared structures

5V6J · Glycan binding protein Y3 from mushroom Coprinus comatus possesses anti-leukemic activity · the same entry in another collection · chain A against A, 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
Every structure of UniProt G3BK00
Elsewhere: RCSB PDB 5V6J · PDBe 5V6J · UniProt G3BK00

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