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Crystal structure of arabidopsis thaliana peptide deformylase 1B (ATPDF1B) in complex with actinonin

Analyse Crystal structure of arabidopsis thaliana peptide deformylase 1B (ATPDF1B) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3M6P
Type: protein
Length: 360 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide deformylase 1B
EC: 3.5.1.88
UniProt: Q9FUZ2
Ligands: BB2, ZN
Pockets: 3 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Peptide deformylase 1B (EC 3.5.1.88)	protein	180	35% helix, 28% strand	Q9FUZ2

Ligands and binding sites

BB2 · Actinonin · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 9 copies · chains A, B

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

Pockets

3 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	134	0.53	0.81	24	BB2
2	134	0.52	0.81	23	BB2
3	89	0.33	0.73	20	ZN

Interfaces

1 interface between chains.

A–B · 639 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3M6P · Crystal structure of Arabidopsis thaliana peptide deformylase 1B (AtPDF1B) in complex… · the same entry in another collection · chain A against A, TM-score 1.00
Q9FUZ2 · AlphaFold monomer V2.0 prediction for peptide deformylase 1B, CHLOROPLASTIC/MITOCHONDRIAL… · a predicted model of the same protein · chain A against A, TM-score 0.99

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9FUZ2
Elsewhere: RCSB PDB 3M6P · PDBe 3M6P · UniProt Q9FUZ2

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