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The complex structure of ATRM5 and trnacys

Analyse The complex structure of ATRM5 and trnacys in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ZZN
Type: protein + RNA
Length: 813 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein MJ0883; RNA (71-mer)
UniProt: Q58293
Ligands: SAM, MG
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 29% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uncharacterized protein MJ0883	protein	336	29% helix, 32% strand	Q58293
B	Uncharacterized protein MJ0883	protein	335	28% helix, 33% strand	Q58293
C, D	RNA (71-mer)	rna	71	—	—

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · 2 copies · chains A, C, B, D
MG · Magnesium ion · metal · 7 copies · chains C, D

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	683	0.83	0.88	70	SAM, MG
2	948	0.80	0.82	63	MG
3	399	0.76	0.86	39	empty
4	74	0.75	0.99	18	empty
5	178	0.74	0.91	39	empty

Interfaces

5 interfaces between chains.

A–C · 2244 Å² buried · 64 hydrogen bonds · protein-nucleic
B–D · 2116 Å² buried · 41 hydrogen bonds · protein-nucleic
B–C · 484 Å² buried · 9 hydrogen bonds · protein-nucleic
A–B · 332 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 170 Å² buried · 4 hydrogen bonds · protein-nucleic

Compared structures

2ZZN · The complex structure of aTrm5 and tRNACys · the same entry in another collection · chain D against D, TM-score 1.00
Q58293 · AlphaFold monomer V2.0 prediction for tRNA (GUANINE(37)-N1)-methyltransferase TRM5B… · a predicted model of the same protein · chain B against A, TM-score 0.82

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 Q58293
Elsewhere: RCSB PDB 2ZZN · PDBe 2ZZN · UniProt Q58293

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