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Crystal structure of S-adenosylmethionine-dependent methyltransferase sibl in its apo form

Analyse Crystal structure of S-adenosylmethionine-dependent methyltransferase sibl in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4QVG
Type: protein
Length: 1,370 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sibl
UniProt: C0LTM6
Pockets: 12 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 51% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sibl	protein	341	52% helix, 18% strand	C0LTM6
B, D	Sibl	protein	340	51% helix, 15% strand	C0LTM6
C	Sibl	protein	349	51% helix, 16% strand	C0LTM6

Pockets

12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	634	0.81	0.86	59	empty
2	929	0.77	0.79	72	empty
3	821	0.75	0.79	45	empty
4	710	0.71	0.78	52	empty
5	417	0.68	0.80	54	empty

Interfaces

5 interfaces between chains.

B–C · 3580 Å² buried · 18 hydrogen bonds · protein-protein
B–D · 312 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 287 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 264 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 261 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4QVG · Crystal structure of S-adenosylmethionine-dependent methyltransferase SibL in its apo form · the same entry in another collection · chain D against D, 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 C0LTM6
Elsewhere: RCSB PDB 4QVG · PDBe 4QVG · UniProt C0LTM6

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