MolNFT v1 · #1518 · protein

Dcmp hydroxymethylase from T4 (phosphate-bound)

1B49 · Protein (deoxycytidylate hydroxymethylase): “Dcmp hydroxymethylase from T4 (phosphate-bound)”. X-ray diffraction, 1 ligand (PO4), 3 pockets (best druggability 0.75). MolNFT v1 #1518 on GenesisL1: 3D structure, binding sites and…

PDB: 1B49
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: PO4
Pockets: 3 · best druggability 0.75

Structure

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

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

Ligands and binding sites

PO4 · Phosphate ion · ion · 2 copies · chains A, C

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	462	0.75	0.84	39	PO4
2	444	0.74	0.83	35	PO4
3	52	0.26	0.73	14	empty

Interfaces

1 interface between chains.

A–C · 2673 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

1B49 · Dcmp hydroxymethylase from T4 (phosphate-bound) · 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 1B49 · PDBe 1B49 · UniProt P08773

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