MolNFT v1 · #57057 · protein

Pyrobaculum aerophilum splicing endonuclease

2ZYZ · Putative uncharacterized protein PAE0789: “Pyrobaculum aerophilum splicing endonuclease”. X-ray diffraction, 9 pockets (best druggability 0.85). MolNFT v1 #57057 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2ZYZ
Type: protein
Length: 555 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative uncharacterized protein PAE0789; TRNA-splicing endonuclease
EC: 3.1.27.9
UniProt: Q8ZYG6, Q8ZVI1
Pockets: 9 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 30% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative uncharacterized protein PAE0789	protein	93	27% helix, 38% strand	Q8ZYG6
B, D	TRNA-splicing endonuclease (EC 3.1.27.9)	protein	183	33% helix, 26% strand	Q8ZVI1
C	Putative uncharacterized protein PAE0789	protein	96	26% helix, 36% strand	Q8ZYG6

Pockets

9 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	628	0.85	0.90	69	empty
2	281	0.65	0.82	37	empty
3	326	0.64	0.80	41	empty
4	131	0.45	0.77	25	empty
5	136	0.42	0.75	35	empty

Interfaces

5 interfaces between chains.

C–D · 1710 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1467 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 795 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 786 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 662 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

2ZYZ · Pyrobaculum aerophilum splicing endonuclease · the same entry in another collection · chain A against A, TM-score 1.00
Q8ZVI1 · AlphaFold monomer V2.0 prediction for tRNA-splicing endonuclease (Q8ZVI1) · a predicted model of the same protein · chain D against A, TM-score 0.94

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 Q8ZYG6
Every structure of UniProt Q8ZVI1
Elsewhere: RCSB PDB 2ZYZ · PDBe 2ZYZ · UniProt Q8ZYG6 · UniProt Q8ZVI1

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.