MolNFT v1 · #21617 · protein

Crystal structure of thermotoga maritima protein hemk, an N5-glutamine methyltransferase

1SG9 · Hemk protein: “Crystal structure of thermotoga maritima protein hemk, an N5-glutamine methyltransferase”. X-ray diffraction, 2 ligands (SAM, GLN), 8 pockets (best druggability 0.71). MolNFT v1 #21617 on GenesisL1: 3D structure…

PDB: 1SG9
Type: protein
Length: 822 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemk protein
UniProt: Q9WYV8
Ligands: SAM, GLN
Pockets: 8 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Hemk protein	protein	274	43% helix, 17% strand	Q9WYV8

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · 3 copies · chains A, B, C
GLN · Glutamine · ligand · 3 copies · chains A, B, C

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

Pockets

8 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	591	0.71	0.79	78	SAM, GLN
2	471	0.70	0.80	67	SAM, GLN
3	380	0.69	0.82	55	SAM, GLN
4	614	0.69	0.78	53	empty
5	108	0.42	0.77	17	empty

Interfaces

2 interfaces between chains.

A–C · 1018 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 272 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1SG9 · Crystal structure of Thermotoga maritima protein HEMK, an N5-glutamine methyltransferase · the same entry in another collection · chain A against A, TM-score 1.00
Q9WYV8 · AlphaFold monomer V2.0 prediction for release factor glutamine methyltransferase (Q9WYV8) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q9WYV8
Elsewhere: RCSB PDB 1SG9 · PDBe 1SG9 · UniProt Q9WYV8

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