Research workbench

Crystal structure of S62A MIF2 mutant

Analyse Crystal structure of S62A MIF2 mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7MRU
Type: protein
Length: 351 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-dopachrome decarboxylase
EC: 4.1.1.84
UniProt: P30046
Pockets: 5 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	D-dopachrome decarboxylase (EC 4.1.1.84)	protein	117	40% helix, 32% strand	P30046

Ligands and binding sites

TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	379	0.75	0.86	39	TRS
2	84	0.50	0.83	16	empty
3	68	0.49	0.84	17	empty
4	79	0.43	0.79	17	empty
5	56	0.30	0.75	12	empty

Interfaces

3 interfaces between chains.

A–B · 1150 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 1133 Å² buried · 21 hydrogen bonds · protein-protein
B–C · 1112 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

7MRU · Crystal structure of S62A MIF2 mutant · the same entry in another collection · chain A against A, TM-score 1.00
P30046 · AlphaFold monomer V2.0 prediction for D-dopachrome decarboxylase (P30046) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P30046
Elsewhere: RCSB PDB 7MRU · PDBe 7MRU · UniProt P30046

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