MolNFT v1 · #121613 · protein

Crystal structure of DR2231_E79A mutant in complex with dump

5I0M: “Crystal structure of DR2231_E79A mutant in complex with dump”. X-ray diffraction, 1 ligand (UMP), 5 pockets (best druggability 0.81). MolNFT v1 #121613 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5I0M
Type: protein
Length: 510 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DR2231
UniProt: Q9RS96
Ligands: UMP
Pockets: 5 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 68% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DR2231	protein	137	64% helix, 1% strand	Q9RS96
C, D	DR2231	protein	118	73% helix, 0% strand	Q9RS96

Ligands and binding sites

UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 copies · chains A, D, 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	1025	0.81	0.83	103	UMP
2	70	0.38	0.78	17	empty
3	79	0.37	0.77	17	empty
4	73	0.36	0.77	19	empty
5	67	0.34	0.77	19	empty

Interfaces

6 interfaces between chains.

A–D · 3018 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 2977 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 166 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 128 Å² buried · 1 hydrogen bond · protein-protein
B–D · 125 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5I0M · Crystal structure of DR2231_E79A mutant in complex with dUMP · 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 5I0M · PDBe 5I0M · UniProt Q9RS96

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