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Structure of leishmania donovani ump synthase

Analyse Structure of leishmania donovani ump synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3QW4
Type: protein
Length: 892 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ump synthase
EC: 2.4.2.10, 4.1.1.23
UniProt: E9BCQ9
Ligands: U5P, CL
Pockets: 10 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Ump synthase (EC 2.4.2.10, 4.1.1.23)	protein	445	43% helix, 20% strand	E9BCQ9
C	Ump synthase (EC 2.4.2.10, 4.1.1.23)	protein	447	45% helix, 20% strand	E9BCQ9

Ligands and binding sites

U5P · Uridine-5'-monophosphate · ligand · 3 copies · chains B, C
CL · Chloride ion · ion · chains C

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

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	111	0.75	0.95	30	U5P
2	353	0.66	0.80	45	U5P
3	177	0.65	0.85	35	U5P
4	429	0.57	0.74	35	empty
5	223	0.57	0.79	30	empty

Interfaces

1 interface between chains.

B–C · 2237 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

3QW4 · Structure of Leishmania donovani UMP synthase · the same entry in another collection · chain B against B, 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 E9BCQ9
Elsewhere: RCSB PDB 3QW4 · PDBe 3QW4 · UniProt E9BCQ9

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