MolNFT v1 · #121486 · protein

Crystal structure of DR2231_E46A mutant in complex with dump and magnesium

5HX1: “Crystal structure of DR2231_E46A mutant in complex with dump and magnesium”. X-ray diffraction, 2 ligands (UMP, MG), 8 pockets (best druggability 0.74). MolNFT v1 #121486 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5HX1
Type: protein
Length: 537 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DR2231
UniProt: Q9RS96
Ligands: UMP, MG
Pockets: 8 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 67% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DR2231	protein	138	63% helix, 1% strand	Q9RS96
C	DR2231	protein	130	69% helix, 0% strand	Q9RS96
D	DR2231	protein	131	68% helix, 0% strand	Q9RS96

Ligands and binding sites

UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 copies · chains A, C, B, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	478	0.74	0.82	51	UMP
2	419	0.73	0.83	47	UMP
3	79	0.37	0.77	19	empty
4	73	0.37	0.78	18	empty
5	61	0.37	0.79	16	empty

Interfaces

6 interfaces between chains.

A–C · 3010 Å² buried · 22 hydrogen bonds · protein-protein
B–D · 3005 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 223 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 155 Å² buried · 1 hydrogen bond · protein-protein
A–D · 134 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5HX1 · Crystal structure of DR2231_E46A mutant in complex with dUMP and magnesium · 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 Q9RS96
Elsewhere: RCSB PDB 5HX1 · PDBe 5HX1 · UniProt Q9RS96

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