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Complex structure of lf-transferase and peptide B

Analyse Complex structure of lf-transferase and peptide B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2Z3N
Type: protein
Length: 470 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: LEUCYL/PHENYLALANYL-tRNA-protein transferase; Peptide (PHE)(ARG)(TYR)(LEU)(GLY)
EC: 2.3.2.6
UniProt: P0A8P1
Pockets: 2 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	LEUCYL/PHENYLALANYL-tRNA-protein transferase (EC 2.3.2.6)	protein	230	34% helix, 26% strand	P0A8P1
C, D	Peptide (PHE)(ARG)(TYR)(LEU)(GLY)	protein	5	60% helix, 0% strand	—

Ligands and binding sites

TAR · D(-)-tartaric acid · additive · 2 copies · chains A, B

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

Pockets

2 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	570	0.79	0.85	55	empty
2	53	0.28	0.75	17	TAR

Interfaces

3 interfaces between chains.

A–B · 882 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 650 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 633 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

2Z3N · complex structure of LF-transferase and peptide B · the same entry in another collection · chain A against A, TM-score 1.00
P0A8P1 · AlphaFold monomer V2.0 prediction for LEUCYL/PHENYLALANYL-tRNA-- protein transferase… · a predicted model of the same protein · chain A 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 P0A8P1
Elsewhere: RCSB PDB 2Z3N · PDBe 2Z3N · UniProt P0A8P1

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