GL1X · GenesisL1 explorer

Research workbench

Crystal structure of type 2 pdf from streptococcus agalactiae in complex with tripeptide met-ala-arg

Analyse Crystal structure of type 2 pdf from streptococcus agalactiae in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5JF0
Type
protein
Length
206 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Peptide deformylase; Met-ala-arg
EC
3.5.1.88
UniProt
Q8E378
Ligands
NI

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 24% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
APeptide deformylase (EC 3.5.1.88)protein20330% helix, 24% strandQ8E378
DMet-ala-argprotein30% helix, 33% strand—

Ligands and binding sites

  • NI · Nickel (II) ion · metal · 8 copies · chains A, D
  • ACT · Acetate ion · additive · chains A

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

Interfaces

1 interface between chains.

  • A–D · 365 Ų buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (nonstandard, oxidation).

Compared structures

  • 5JF0 · Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with tripeptide… · the same entry in another collection · chain A against A, TM-score 1.00
  • Q8E378 · AlphaFold monomer V2.0 prediction for peptide deformylase (Q8E378) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

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