MolNFT v1 · #51945 · protein

Structure of the wild-type discoidin II from dictyostelium discoideum

2VME · Discoidin-2: “Structure of the wild-type discoidin II from dictyostelium discoideum”. X-ray diffraction, 3 ligands (CA, ZN, CL), 9 pockets (best druggability 0.86). MolNFT v1 #51945 on GenesisL1: 3D structure, binding sites and…

PDB: 2VME
Type: protein
Length: 1,534 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Discoidin-2
UniProt: P42530
Ligands: CA, ZN, CL
Pockets: 9 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E	Discoidin-2	protein	256	4% helix, 51% strand	P42530
C, F	Discoidin-2	protein	255	4% helix, 51% strand	P42530

Ligands and binding sites

CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
ZN · Zinc ion · metal · 2 copies · chains A, B, C, D, E, F
CL · Chloride ion · ion · 2 copies · chains A, B, C, D, E, F
GOL · Glycerol · additive · 15 copies · chains A, C, B, D, E, F
PG4 · Tetraethylene glycol · additive · chains B, C

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

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	761	0.86	0.89	87	empty
2	488	0.86	0.93	54	empty
3	508	0.86	0.92	56	empty
4	701	0.86	0.90	85	empty
5	993	0.71	0.75	80	empty

Interfaces

7 interfaces between chains.

B–C · 2094 Å² buried · 38 hydrogen bonds · protein-protein
D–E · 2081 Å² buried · 40 hydrogen bonds · protein-protein
E–F · 2077 Å² buried · 35 hydrogen bonds · protein-protein
A–B · 2053 Å² buried · 34 hydrogen bonds · protein-protein
D–F · 1974 Å² buried · 39 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (phosphorylation).

Compared structures

2VME · Structure of the wild-type discoidin II from Dictyostelium discoideum · the same entry in another collection · chain F against F, 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 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 P42530
Elsewhere: RCSB PDB 2VME · PDBe 2VME · UniProt P42530

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