MolNFT v1 · #123275 · protein
Crystal structure of type 2 pdf from streptococcus agalactiae in complex with tripeptide met-ala-arg
5JF0 · Peptide deformylase: “Crystal structure of type 2 pdf from streptococcus agalactiae in complex with tripeptide met-ala-arg”. X-ray diffraction, 1 ligand (NI). MolNFT v1 #123275 on GenesisL1: 3D structure, binding sites and pockets…
- 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).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase (EC 3.5.1.88) | protein | 203 | 30% helix, 24% strand | Q8E378 |
| D | Met-ala-arg | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
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
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q8E378
- Elsewhere: RCSB PDB 5JF0 · PDBe 5JF0 · UniProt Q8E378
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.