Research workbench

Crystal structure of milb complexed with cytidine 5'-monophosphate

Analyse Crystal structure of milb complexed with cytidine 5'-monophosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4JEM
Type: protein
Length: 310 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CMP/HYDROXYMETHYL cmp hydrolase
UniProt: B4Y381
Ligands: C5P
Pockets: 6 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CMP/HYDROXYMETHYL cmp hydrolase	protein	157	46% helix, 18% strand	B4Y381
B	CMP/HYDROXYMETHYL cmp hydrolase	protein	153	49% helix, 18% strand	B4Y381

Ligands and binding sites

C5P · Cytidine-5'-monophosphate · ligand · 2 copies · chains A, B

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

Pockets

6 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	179	0.71	0.89	34	C5P
2	189	0.64	0.84	33	C5P
3	59	0.48	0.85	17	empty
4	80	0.41	0.78	16	empty
5	70	0.40	0.79	16	empty

Interfaces

1 interface between chains.

A–B · 1188 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4JEM · Crystal structure of MilB complexed with cytidine 5'-monophosphate · 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 B4Y381
Elsewhere: RCSB PDB 4JEM · PDBe 4JEM · UniProt B4Y381

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