MolNFT v1 · #103256 · protein

Structure of vccnt-7C8C bound to 5-fluorouridine

4PB2 · Nupc family protein: “Structure of vccnt-7C8C bound to 5-fluorouridine”. X-ray diffraction, 2 ligands (5UD, NA), 5 pockets (best druggability 0.66). MolNFT v1 #103256 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4PB2
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: 5UD, NA
Pockets: 5 · best druggability 0.66

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

5UD · 5-fluorouridine · 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

5 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	444	0.66	0.78	41	5UD
2	161	0.63	0.84	19	empty
3	130	0.44	0.76	20	empty
4	67	0.34	0.76	17	empty
5	66	0.30	0.73	14	empty

Compared structures

4PB2 · Structure of vcCNT-7C8C bound to 5-fluorouridine · 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 4PB2 · PDBe 4PB2 · UniProt Q9KPL5

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