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XFEL structure of T4dCH D179N mutant complex with natively expressed dTMP

Analyse XFEL structure of T4dCH D179N mutant complex with natively expressed dTMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6L18
Type: protein
Length: 246 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.9
Source: Enterobacteria phage T4
Molecule: Deoxycytidylate 5-hydroxymethyltransferase
EC: 2.1.2.8
UniProt: P08773
Ligands: TMP, NA, IOD
Pockets: 1 · best druggability 0.73

Structure

x-ray diffraction · resolution 1.9 · 1 distinct chain · 41% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Deoxycytidylate 5-hydroxymethyltransferase (EC 2.1.2.8)	protein	246	41% helix, 22% strand	P08773

Ligands and binding sites

TMP · Thymidine-5'-phosphate · ligand · chains A
NA · Sodium ion · metal · chains A
IOD · Iodide ion · ion · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	514	0.73	0.81	38	TMP

Compared structures

6L18 · Xfel structure of T4DCH D179N mutant complex with natively expressed dtmp · the same entry in another collection · chain A against A, TM-score 1.00

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 P08773
Elsewhere: RCSB PDB 6L18 · PDBe 6L18 · UniProt P08773

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