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Heptameric crystal structure of MTH649, an sm-like archaeal protein from methanobacterium thermautotrophicum

Analyse Heptameric crystal structure of MTH649, an sm-like archaeal protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1JBM
Type: protein
Length: 521 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative snrnp sm-like protein
UniProt: O26745
Pockets: 8 · best druggability 0.45

Structure

x-ray diffraction · 7 distinct chains · 13% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative snrnp sm-like protein	protein	78	9% helix, 55% strand	O26745
B	Putative snrnp sm-like protein	protein	73	14% helix, 55% strand	O26745
C	Putative snrnp sm-like protein	protein	77	13% helix, 55% strand	O26745
D	Putative snrnp sm-like protein	protein	71	15% helix, 58% strand	O26745
E	Putative snrnp sm-like protein	protein	75	13% helix, 55% strand	O26745
F	Putative snrnp sm-like protein	protein	73	15% helix, 59% strand	O26745
G	Putative snrnp sm-like protein	protein	74	12% helix, 55% strand	O26745

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 11 copies · chains C, B, D, E, F, G
ACY · Acetic acid · additive · 5 copies · chains A, B, C, D, E, F, G

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

Pockets

8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	199	0.45	0.74	42	EDO
2	69	0.44	0.82	16	EDO
3	56	0.43	0.82	14	ACY, EDO
4	80	0.41	0.79	17	empty
5	54	0.36	0.79	14	ACY, EDO

Interfaces

7 interfaces between chains.

E–F · 935 Å² buried · 22 hydrogen bonds · protein-protein
A–G · 893 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 892 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 879 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 823 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

1JBM · Heptameric crystal structure of Mth649, an Sm-like archaeal protein from Methanobacterium… · the same entry in another collection · chain G against G, TM-score 1.00
O26745 · AlphaFold monomer V2.0 prediction for putative snrnp sm-like protein (O26745) · a predicted model of the same protein · chain E against A, TM-score 0.95

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 O26745
Elsewhere: RCSB PDB 1JBM · PDBe 1JBM · UniProt O26745

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