MolNFT v1 · #18570 · protein

Crystal structure of the apo-form of the yfdw gene product of E. COLI

1PT7 · Hypothetical protein yfdw: “Crystal structure of the apo-form of the yfdw gene product of E. COLI”. X-ray diffraction, 1 ligand (PO4), 8 pockets (best druggability 0.78). MolNFT v1 #18570 on GenesisL1: 3D structure, binding sites…

PDB: 1PT7
Type: protein
Length: 830 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein yfdw
UniProt: P69902
Ligands: PO4
Pockets: 8 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Hypothetical protein yfdw	protein	415	40% helix, 14% strand	P69902

Ligands and binding sites

PO4 · Phosphate ion · ion · 8 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

8 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	709	0.78	0.82	89	PO4
2	839	0.77	0.81	114	PO4
3	149	0.48	0.78	27	empty
4	128	0.48	0.79	19	empty
5	91	0.34	0.75	27	empty

Interfaces

1 interface between chains.

A–B · 6254 Å² buried · 80 hydrogen bonds · protein-protein

Compared structures

1PT7 · Crystal structure of the apo-form of the yfdW gene product of E. coli · the same entry in another collection · chain A against A, TM-score 1.00
P69902 · AlphaFold monomer V2.0 prediction for formyl-COA:OXALATE CoA- transferase (P69902) · 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 P69902
Elsewhere: RCSB PDB 1PT7 · PDBe 1PT7 · UniProt P69902

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