Research workbench

X-ray structure of thermococcus gammatolerans mcrb aaa+ domain hexamer in P21 symmetry

Analyse X-ray structure of thermococcus gammatolerans mcrb aaa+ domain hexamer in P21… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6UT3
Type: protein
Length: 2,061 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTPase subunit of restriction endonuclease
UniProt: C5A3Z3
Ligands: GSP, MG
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 6 distinct chains · 37% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTPase subunit of restriction endonuclease	protein	321	16% helix, 1% strand	C5A3Z3
B	GTPase subunit of restriction endonuclease	protein	365	36% helix, 15% strand	C5A3Z3
C	GTPase subunit of restriction endonuclease	protein	375	43% helix, 12% strand	C5A3Z3
D	GTPase subunit of restriction endonuclease	protein	381	43% helix, 14% strand	C5A3Z3
E	GTPase subunit of restriction endonuclease	protein	384	43% helix, 13% strand	C5A3Z3
F	GTPase subunit of restriction endonuclease	protein	235	36% helix, 17% strand	C5A3Z3

Ligands and binding sites

GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 4 copies · chains B, C, D, E, F
MG · Magnesium ion · metal · 4 copies · chains B, C, D, E, F

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	1029	0.87	0.88	115	empty
2	823	0.86	0.88	129	empty
3	490	0.83	0.90	71	empty
4	309	0.81	0.91	57	empty
5	806	0.81	0.84	91	empty

Interfaces

6 interfaces between chains.

D–E · 2726 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 2716 Å² buried · 27 hydrogen bonds · protein-protein
B–C · 2484 Å² buried · 20 hydrogen bonds · protein-protein
E–F · 2150 Å² buried · 17 hydrogen bonds · protein-protein
A–F · 980 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6UT3 · X-ray structure of Thermococcus gammatolerans McrB AAA+ domain hexamer in P21 symmetry · 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 C5A3Z3
Elsewhere: RCSB PDB 6UT3 · PDBe 6UT3 · UniProt C5A3Z3

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.