MolNFT v1 · #113021 · protein

Crystal structure of mtpap in complex with UTP

5A2Y · Mitochondrial protein: “Crystal structure of mtpap in complex with UTP”. X-ray diffraction, 2 ligands (UTP, MG), 11 pockets (best druggability 0.70). MolNFT v1 #113021 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5A2Y
Type: protein
Length: 932 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mitochondrial protein
UniProt: F1NBW0
Ligands: UTP, MG
Pockets: 11 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mitochondrial protein	protein	468	41% helix, 18% strand	F1NBW0
B	Mitochondrial protein	protein	464	40% helix, 18% strand	F1NBW0

Ligands and binding sites

UTP · Uridine 5'-triphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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	839	0.70	0.76	61	UTP, MG
2	693	0.67	0.75	50	UTP, MG
3	135	0.56	0.82	25	empty
4	119	0.47	0.79	20	empty
5	205	0.46	0.74	31	empty

Interfaces

1 interface between chains.

A–B · 3545 Å² buried · 35 hydrogen bonds · protein-protein

Compared structures

5A2Y · Crystal structure of mtPAP in complex with UTP · 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 F1NBW0
Elsewhere: RCSB PDB 5A2Y · PDBe 5A2Y · UniProt F1NBW0

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