Research workbench

Structure of bstrmb apo

Analyse Structure of bstrmb apo in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7NZJ
Type: protein
Length: 1,228 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA (guanine-N(7)-)-methyltransferase
EC: 2.1.1.33
UniProt: O34522
Ligands: NA
Pockets: 15 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	TRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.33)	protein	206	41% helix, 18% strand	O34522
B, D	TRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.33)	protein	203	40% helix, 19% strand	O34522
C, F	TRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.33)	protein	205	43% helix, 19% strand	O34522

Ligands and binding sites

NA · Sodium ion · metal · chains A, E
GOL · Glycerol · additive · 5 copies · chains B, C, D, A, E

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

Pockets

15 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	1025	0.77	0.79	74	NA, GOL
2	670	0.67	0.76	59	GOL
3	710	0.67	0.75	57	GOL
4	190	0.50	0.76	27	empty
5	218	0.50	0.75	27	empty

Interfaces

6 interfaces between chains.

C–D · 818 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 807 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 804 Å² buried · 14 hydrogen bonds · protein-protein
A–E · 611 Å² buried · 4 hydrogen bonds · protein-protein
D–F · 276 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

7NZJ · Structure of bsTrmB apo · the same entry in another collection · chain F against F, TM-score 1.00
O34522 · AlphaFold monomer V2.0 prediction for tRNA (guanine-N(7)-)-methyltransferase (O34522) · a predicted model of the same protein · chain B 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 O34522
Elsewhere: RCSB PDB 7NZJ · PDBe 7NZJ · UniProt O34522

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