Research workbench

M. tb egtd in complex with imatinib

Analyse M. tb egtd in complex with imatinib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7SF4
Type: protein
Length: 642 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histidine N-alpha-methyltransferase
EC: 2.1.1.44
UniProt: A0A045KE74
Ligands: XDK
Pockets: 4 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Histidine N-alpha-methyltransferase (EC 2.1.1.44)	protein	321	43% helix, 27% strand	A0A045KE74

Ligands and binding sites

XDK · 2-amino-4-pyridyl-pyrimidine · ligand · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
GOL · Glycerol · additive · 6 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1040	0.78	0.80	97	XDK, GOL, EDO
2	917	0.77	0.80	86	XDK, GOL, EDO
3	117	0.37	0.74	17	empty
4	53	0.32	0.77	11	empty

Interfaces

1 interface between chains.

A–B · 105 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7SF4 · M. tb EgtD in complex with imatinib · 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 A0A045KE74
Elsewhere: RCSB PDB 7SF4 · PDBe 7SF4 · UniProt A0A045KE74

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