MolNFT v1 · #2294 · protein

Peptide deformylase as NI2+ containing form

1BS7 · Protein (peptide deformylase): “Peptide deformylase as NI2+ containing form”. X-ray diffraction, 2 ligands (NI, SO4), 4 pockets (best druggability 0.62). MolNFT v1 #2294 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1BS7
Type: protein
Length: 504 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (peptide deformylase)
EC: 3.5.1.31
UniProt: P0A6K3
Ligands: NI, SO4
Pockets: 4 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Protein (peptide deformylase) (EC 3.5.1.31)	protein	168	36% helix, 24% strand	P0A6K3

Ligands and binding sites

NI · Nickel (II) ion · metal · 3 copies · chains A, B, C
SO4 · Sulfate ion · ion · 2 copies · chains B, C

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

Pockets

4 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	534	0.62	0.75	58	NI
2	140	0.50	0.79	26	NI
3	135	0.49	0.79	25	empty
4	130	0.39	0.74	24	empty

Interfaces

2 interfaces between chains.

B–C · 605 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 274 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

1BS7 · Peptide deformylase as NI2+ containing form · the same entry in another collection · chain A against A, TM-score 1.00
P0A6K3 · AlphaFold monomer V2.0 prediction for peptide deformylase (P0A6K3) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P0A6K3
Elsewhere: RCSB PDB 1BS7 · PDBe 1BS7 · UniProt P0A6K3

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