MolNFT v1 · #92144 · protein

Crystal structure of plasmodium falciparum orotate phosphoribosyltransferase

4FYM: “Crystal structure of plasmodium falciparum orotate phosphoribosyltransferase”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.72). MolNFT v1 #92144 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4FYM
Type: protein
Length: 1,747 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Orotate phosphoribosyltransferase
EC: 2.4.2.10
UniProt: Q8N0R1
Ligands: SO4
Pockets: 20 · best druggability 0.72

Structure

x-ray diffraction · 8 distinct chains · 46% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Orotate phosphoribosyltransferase (EC 2.4.2.10)	protein	223	46% helix, 23% strand	Q8N0R1
B	Orotate phosphoribosyltransferase (EC 2.4.2.10)	protein	219	47% helix, 23% strand	Q8N0R1
C	Orotate phosphoribosyltransferase (EC 2.4.2.10)	protein	222	46% helix, 22% strand	Q8N0R1
D	Orotate phosphoribosyltransferase (EC 2.4.2.10)	protein	227	45% helix, 23% strand	Q8N0R1
E	Orotate phosphoribosyltransferase (EC 2.4.2.10)	protein	222	45% helix, 24% strand	Q8N0R1
F	Orotate phosphoribosyltransferase (EC 2.4.2.10)	protein	209	49% helix, 22% strand	Q8N0R1
G	Orotate phosphoribosyltransferase (EC 2.4.2.10)	protein	216	47% helix, 23% strand	Q8N0R1
H	Orotate phosphoribosyltransferase (EC 2.4.2.10)	protein	209	47% helix, 20% strand	Q8N0R1

Ligands and binding sites

SO4 · Sulfate ion · ion · 33 copies · chains A, B, F, C, D, E, H, G

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

Pockets

20 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	621	0.72	0.80	47	SO4
2	572	0.71	0.79	62	SO4
3	448	0.64	0.77	34	empty
4	170	0.60	0.82	17	empty
5	335	0.57	0.76	42	SO4

Interfaces

9 interfaces between chains.

E–H · 1632 Å² buried · 33 hydrogen bonds · protein-protein
A–B · 1579 Å² buried · 30 hydrogen bonds · protein-protein
F–G · 1562 Å² buried · 28 hydrogen bonds · protein-protein
C–D · 1525 Å² buried · 32 hydrogen bonds · protein-protein
D–E · 1250 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

4FYM · Crystal structure of Plasmodium falciparum orotate phosphoribosyltransferase · 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 Q8N0R1
Elsewhere: RCSB PDB 4FYM · PDBe 4FYM · UniProt Q8N0R1

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