MolNFT v1 · #54025 · protein

Structure of yncf in complex with dupnhpp

2XCE · Probable deoxyuridine 5'-triphosphate nucleotidohydrolase…: “Structure of yncf in complex with dupnhpp”. X-ray diffraction, 2 ligands (DUP, CA), 11 pockets (best druggability 0.72). MolNFT v1 #54025 on GenesisL1: 3D structure…

PDB: 2XCE
Type: protein
Length: 774 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable deoxyuridine 5'-triphosphate nucleotidohydrolase yncf
EC: 3.6.1.23
UniProt: O31801
Ligands: DUP, CA
Pockets: 11 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Probable deoxyuridine 5'-triphosphate nucleotidohydrolase yncf (EC 3.6.1.23)	protein	129	4% helix, 47% strand	O31801

Ligands and binding sites

DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · 6 copies · chains A, C, B, F, D, E
CA · Calcium ion · metal · 8 copies · chains A, C, B, F, D, E
GOL · Glycerol · additive · 6 copies · chains A, B, C, D, F, E

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

Pockets

11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	656	0.72	0.79	60	CA, DUP
2	728	0.70	0.77	64	DUP, CA, GOL
3	224	0.56	0.78	44	CA, DUP
4	168	0.50	0.78	27	CA, GOL, DUP
5	146	0.48	0.77	21	CA, DUP

Interfaces

8 interfaces between chains.

E–F · 1596 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 1578 Å² buried · 22 hydrogen bonds · protein-protein
D–E · 1532 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 1518 Å² buried · 22 hydrogen bonds · protein-protein
D–F · 1511 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

2XCE · Structure of YncF in complex with dUpNHpp · the same entry in another collection · chain C against C, TM-score 1.00
O31801 · AlphaFold monomer V2.0 prediction for probable deoxyuridine 5'-triphosphate… · a predicted model of the same protein · chain A against A, TM-score 0.96

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 O31801
Elsewhere: RCSB PDB 2XCE · PDBe 2XCE · UniProt O31801

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