MolNFT v1 · #139500 · protein

Transferase with ligands

5XHP · Putative cytoplasmic protein: “Transferase with ligands”. X-ray diffraction, 3 ligands (ARG, UDP, MN), 5 pockets (best druggability 0.64). MolNFT v1 #139500 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XHP
Type: protein
Length: 606 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative cytoplasmic protein
UniProt: E8XCX6
Ligands: ARG, UDP, MN
Pockets: 5 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
F, E	Putative cytoplasmic protein	protein	303	40% helix, 21% strand	E8XCX6

Ligands and binding sites

ARG · Arginine · ligand · 2 copies · chains F, E
UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains F, E
MN · Manganese (II) ion · metal · 2 copies · chains F, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	536	0.64	0.76	60	empty
2	173	0.46	0.75	27	ARG, MN, UDP
3	98	0.44	0.78	20	empty
4	96	0.44	0.78	21	empty
5	128	0.42	0.76	18	UDP

Interfaces

1 interface between chains.

F–E · 147 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5XHP · Transferase with ligands · the same entry in another collection · chain E against E, 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 E8XCX6
Elsewhere: RCSB PDB 5XHP · PDBe 5XHP · UniProt E8XCX6

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