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Crystal structure of putative rRNA-methylase from clostridium thermocellum

Analyse Crystal structure of putative rRNA-methylase from clostridium thermocellum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3EEY
Type: protein
Length: 1,887 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative rRNA methylase
UniProt: A3DDA2
Ligands: SAM, SO4
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 6 distinct chains · 37% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative rRNA methylase	protein	195	35% helix, 26% strand	A3DDA2
B	Putative rRNA methylase	protein	192	39% helix, 27% strand	A3DDA2
C, D, E, H, J	Putative rRNA methylase	protein	189	39% helix, 26% strand	A3DDA2
F	Putative rRNA methylase	protein	190	34% helix, 27% strand	A3DDA2
G	Putative rRNA methylase	protein	179	38% helix, 26% strand	A3DDA2
I	Putative rRNA methylase	protein	186	39% helix, 25% strand	A3DDA2

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · 9 copies · chains A, B, C, D, E, F, H, I, J
SO4 · Sulfate ion · ion · 5 copies · chains A, D, B, C
GOL · Glycerol · additive · 4 copies · chains A, C, E, B, D, F, I, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	915	0.79	0.81	99	GOL
2	718	0.79	0.83	93	GOL
3	624	0.78	0.84	78	SAM
4	385	0.74	0.85	36	SO4
5	407	0.73	0.83	46	GOL

Interfaces

23 interfaces between chains.

A–C · 1344 Å² buried · 24 hydrogen bonds · protein-protein
B–D · 1324 Å² buried · 24 hydrogen bonds · protein-protein
E–H · 1321 Å² buried · 24 hydrogen bonds · protein-protein
F–I · 1312 Å² buried · 23 hydrogen bonds · protein-protein
G–J · 1306 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

3EEY · CRYSTAL STRUCTURE OF PUTATIVE RRNA-METHYLASE FROM Clostridium thermocellum · the same entry in another collection · chain E against E, 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 A3DDA2
Elsewhere: RCSB PDB 3EEY · PDBe 3EEY · UniProt A3DDA2

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