Research workbench

Apo structure of a thiazolinyl imine reductase from yersinia enterocolitica (IRP3)

Analyse Apo structure of a thiazolinyl imine reductase from yersinia enterocolitica… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4GMF
Type: protein
Length: 1,326 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yersiniabactin biosynthetic protein ybtu
UniProt: A1JTG0
Ligands: SO4
Pockets: 18 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 39% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Yersiniabactin biosynthetic protein ybtu	protein	335	38% helix, 24% strand	A1JTG0
B	Yersiniabactin biosynthetic protein ybtu	protein	329	39% helix, 24% strand	A1JTG0
C	Yersiniabactin biosynthetic protein ybtu	protein	330	39% helix, 25% strand	A1JTG0
D	Yersiniabactin biosynthetic protein ybtu	protein	332	39% helix, 24% strand	A1JTG0

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 2 copies · chains A, B, D
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B, D

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

Pockets

18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1088	0.82	0.83	103	empty
2	106	0.80	0.99	22	empty
3	103	0.79	0.99	18	empty
4	890	0.78	0.81	97	empty
5	933	0.77	0.79	93	EPE

Interfaces

4 interfaces between chains.

A–B · 3382 Å² buried · 35 hydrogen bonds · protein-protein
C–D · 3334 Å² buried · 30 hydrogen bonds · protein-protein
A–C · 553 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 334 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

4GMF · Apo Structure of a Thiazolinyl Imine Reductase from Yersinia enterocolitica (Irp3) · 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 A1JTG0
Elsewhere: RCSB PDB 4GMF · PDBe 4GMF · UniProt A1JTG0

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