MolNFT v1 · #113022 · protein

Crystal structure of mtpap in complex with GTP

5A2Z · Mitochondrial protein: “Crystal structure of mtpap in complex with GTP”. X-ray diffraction, 2 ligands (GTP, MG), 10 pockets (best druggability 0.70). MolNFT v1 #113022 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5A2Z
Type: protein
Length: 928 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mitochondrial protein
UniProt: F1NBW0
Ligands: GTP, MG
Pockets: 10 · 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	466	42% helix, 18% strand	F1NBW0
B	Mitochondrial protein	protein	462	41% helix, 18% strand	F1NBW0

Ligands and binding sites

GTP · Guanosine-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

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	837	0.70	0.76	57	GTP, MG
2	736	0.69	0.76	51	GTP, MG
3	230	0.54	0.77	31	empty
4	83	0.53	0.84	21	empty
5	125	0.49	0.79	20	empty

Interfaces

1 interface between chains.

A–B · 3465 Å² buried · 35 hydrogen bonds · protein-protein

Compared structures

5A2Z · Crystal structure of mtPAP in complex with GTP · 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 5A2Z · PDBe 5A2Z · UniProt F1NBW0

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