Research workbench

D-tyr trnatyr deacylase from escherichia COLI

Analyse D-tyr trnatyr deacylase from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1JKE
Type: protein
Length: 580 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-tyr-trnatyr deacylase
UniProt: P0A6M4
Ligands: ZN
Pockets: 7 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain · 23% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	D-tyr-trnatyr deacylase	protein	145	23% helix, 42% strand	P0A6M4

Ligands and binding sites

ZN · Zinc ion · metal · 12 copies · chains A, C, B, D

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

Pockets

7 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	230	0.60	0.81	35	empty
2	154	0.48	0.77	31	empty
3	121	0.47	0.78	25	empty
4	117	0.46	0.78	24	empty
5	113	0.38	0.75	30	empty

Interfaces

3 interfaces between chains.

A–D · 1778 Å² buried · 51 hydrogen bonds · protein-protein
B–C · 1690 Å² buried · 50 hydrogen bonds · protein-protein
A–C · 615 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

1JKE · D-Tyr tRNATyr deacylase from Escherichia coli · the same entry in another collection · chain D against D, TM-score 1.00
P0A6M4 · AlphaFold monomer V2.0 prediction for D-aminoacyl-tRNA deacylase (P0A6M4) · a predicted model of the same protein · chain D 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 P0A6M4
Elsewhere: RCSB PDB 1JKE · PDBe 1JKE · UniProt P0A6M4

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