MolNFT v1 · #189874 · protein

Crystal structure of yfih with C107A mutation in complex with udp- murnac-L-serine

7W1G · Purine nucleoside phosphorylase yfih: “Crystal structure of yfih with C107A mutation in complex with udp- murnac-L-serine”. X-ray diffraction, 3 ligands (EPZ, 87E, SO4), 14 pockets (best druggability 0.72). MolNFT v1 #189874 on…

PDB: 7W1G
Type: protein
Length: 970 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Purine nucleoside phosphorylase yfih
EC: 3.5.4.4
UniProt: P33644
Ligands: EPZ, 87E, SO4
Pockets: 14 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 25% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Purine nucleoside phosphorylase yfih (EC 3.5.4.4)	protein	242	25% helix, 25% strand	P33644
C, D	Purine nucleoside phosphorylase yfih (EC 3.5.4.4)	protein	243	25% helix, 25% strand	P33644

Ligands and binding sites

EPZ · (2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy) phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoic acid · ligand · 2 copies · chains A, B
87E · (2S)-2-[[(2R)-2-[(2R,3R,4R,5S,6R)-3-acetamido-2-[[[(2R, 3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3, 4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-6-(hydroxymethyl)-5-oxidanyl-oxan-4-yl]oxypropanoyl]amino]-3-oxidanyl-propanoic acid · ligand · 2 copies · chains C, D
SO4 · Sulfate ion · ion · 2 copies · chains A, B
ACT · Acetate ion · additive · 3 copies · chains B, C
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B

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

Pockets

14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	276	0.72	0.86	50	empty
2	452	0.68	0.80	58	empty
3	334	0.67	0.81	38	empty
4	194	0.64	0.84	25	empty
5	228	0.56	0.78	28	EPZ, SO4

Interfaces

4 interfaces between chains.

A–B · 928 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 916 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 465 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 60 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7W1G · Crystal structure of YfiH with C107A mutation in complex with UDP-MurNAc-L-Serine · the same entry in another collection · chain A against A, TM-score 1.00
P33644 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase yfih (P33644) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 P33644
Elsewhere: RCSB PDB 7W1G · PDBe 7W1G · UniProt P33644

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