MolNFT v1 · #109763 · protein

Crystal structure of an octadecameric TF55 complex from S. solfataricus

4XCD · Thermosome subunit beta: “Crystal structure of an octadecameric TF55 complex from S. solfataricus”. X-ray diffraction, 1 ligand (ADP), 20 pockets (best druggability 0.80). MolNFT v1 #109763 on GenesisL1: 3D structure, binding sites…

PDB: 4XCD
Type: protein
Length: 3,016 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thermosome subunit beta
UniProt: Q9V2T8
Ligands: ADP
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 6 distinct chains · 49% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thermosome subunit beta	protein	507	49% helix, 17% strand	Q9V2T8
B	Thermosome subunit beta	protein	500	49% helix, 17% strand	Q9V2T8
C	Thermosome subunit beta	protein	505	49% helix, 16% strand	Q9V2T8
D	Thermosome subunit beta	protein	503	49% helix, 17% strand	Q9V2T8
E	Thermosome subunit beta	protein	501	49% helix, 18% strand	Q9V2T8
F	Thermosome subunit beta	protein	500	49% helix, 16% strand	Q9V2T8

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, 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	970	0.80	0.81	114	ADP
2	959	0.79	0.81	101	ADP
3	895	0.79	0.81	98	ADP
4	867	0.78	0.81	92	ADP
5	839	0.78	0.81	54	empty

Interfaces

6 interfaces between chains.

B–C · 999 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 927 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 832 Å² buried · 7 hydrogen bonds · protein-protein
D–E · 766 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 647 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4XCD · Crystal structure of an octadecameric TF55 complex from S. solfataricus · the same entry in another collection · chain F against F, TM-score 1.00
Q9V2T8 · AlphaFold monomer V2.0 prediction for thermosome subunit beta (Q9V2T8) · a predicted model of the same protein · chain F against A, TM-score 0.97

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 Q9V2T8
Elsewhere: RCSB PDB 4XCD · PDBe 4XCD · UniProt Q9V2T8

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