MolNFT v1 · #51940 · protein

Native structure of the recombinant discoidin II of dictyostelium discoideum at 1.75 ångström

2VM9 · Discoidin-2: “Native structure of the recombinant discoidin II of dictyostelium discoideum at 1.75 ångström”. X-ray diffraction, 3 ligands (CA, PO4, CL), 1 pocket (best druggability 0.27). MolNFT v1 #51940 on GenesisL1: 3D…

PDB: 2VM9
Type: protein
Length: 252 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Discoidin-2
UniProt: P42530
Ligands: CA, PO4, CL
Pockets: 1 · best druggability 0.27

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Discoidin-2	protein	252	4% helix, 50% strand	P42530

Ligands and binding sites

CA · Calcium ion · metal · chains A
PO4 · Phosphate ion · ion · 3 copies · chains A
CL · Chloride ion · ion · 3 copies · chains A
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A

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	57	0.27	0.73	17	empty

Compared structures

2VM9 · Native structure of the recombinant discoidin II of Dictyostelium discoideum at 1.75… · the same entry in another collection · chain A against A, TM-score 1.00
P42530 · AlphaFold monomer V2.0 prediction for discoidin-2 (P42530) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P42530
Elsewhere: RCSB PDB 2VM9 · PDBe 2VM9 · UniProt P42530

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