MolNFT v1 · #1558 · protein

Dcmp hydroxymethylase from T4

1B5E · Protein (deoxycytidylate hydroxymethylase): “Dcmp hydroxymethylase from T4”. X-ray diffraction, 1 ligand (DCM), 3 pockets (best druggability 0.77). MolNFT v1 #1558 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1B5E
Type: protein
Length: 482 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (deoxycytidylate hydroxymethylase)
EC: 2.1.2.8
UniProt: P08773
Ligands: DCM
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein (deoxycytidylate hydroxymethylase) (EC 2.1.2.8)	protein	241	41% helix, 23% strand	P08773

Ligands and binding sites

DCM · 2'-deoxycytidine-5'-monophosphate · ligand · 2 copies · chains A, B

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

Pockets

3 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	414	0.77	0.86	41	DCM
2	462	0.75	0.84	45	DCM
3	58	0.27	0.73	15	empty

Interfaces

1 interface between chains.

A–B · 2691 Å² buried · 41 hydrogen bonds · protein-protein

Compared structures

1B5E · Dcmp hydroxymethylase from T4 · 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 1B5E · PDBe 1B5E · UniProt P08773

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