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Structure of vccnt-7C8C bound to pyrrolo-cytidine

Analyse Structure of vccnt-7C8C bound to pyrrolo-cytidine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4PD8
Type: protein
Length: 404 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nupc family protein
UniProt: Q9KPL5
Ligands: P0C, NA
Pockets: 6 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 78% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nupc family protein	protein	404	78% helix, 0% strand	Q9KPL5

Ligands and binding sites

P0C · 6-methyl-3-(beta-D-ribofuranosyl)-3,7-dihydro-2H-pyrrolo[2,3-d]pyrimidin-2-one · ligand · chains A
NA · Sodium ion · metal · chains A
DMU · Decyl-beta-D-maltopyranoside · additive · chains A

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	390	0.65	0.79	41	P0C
2	170	0.61	0.83	20	empty
3	132	0.46	0.76	18	empty
4	63	0.35	0.77	17	empty
5	72	0.34	0.75	16	empty

Compared structures

4PD8 · Structure of vcCNT-7C8C bound to pyrrolo-cytidine · 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 Q9KPL5
Elsewhere: RCSB PDB 4PD8 · PDBe 4PD8 · UniProt Q9KPL5

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