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Crystal structure of the 11S subunit of the plasmodium falciparum proteasome, PA28

Analyse Crystal structure of the 11S subunit of the plasmodium falciparum proteasome… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6DFK
Type: protein
Length: 3,125 residues
Chains: 14
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Subunit of proteaseome activator COMPLEX,PUTATIVE
UniProt: Q8I374
Ligands: SO4
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 14 distinct chains · 68% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Subunit of proteaseome activator COMPLEX,PUTATIVE	protein	216	70% helix, 1% strand	Q8I374
B	Subunit of proteaseome activator COMPLEX,PUTATIVE	protein	232	66% helix, 4% strand	Q8I374
C	Subunit of proteaseome activator COMPLEX,PUTATIVE	protein	222	68% helix, 3% strand	Q8I374
D	Subunit of proteaseome activator COMPLEX,PUTATIVE	protein	233	65% helix, 4% strand	Q8I374
E	Subunit of proteaseome activator COMPLEX,PUTATIVE	protein	212	72% helix, 1% strand	Q8I374
F	Subunit of proteaseome activator COMPLEX,PUTATIVE	protein	229	66% helix, 4% strand	Q8I374
G	Subunit of proteaseome activator COMPLEX,PUTATIVE	protein	213	71% helix, 1% strand	Q8I374
H	Subunit of proteaseome activator COMPLEX,PUTATIVE	protein	216	70% helix, 3% strand	Q8I374
I	Subunit of proteaseome activator COMPLEX,PUTATIVE	protein	236	64% helix, 4% strand	Q8I374
J	Subunit of proteaseome activator COMPLEX,PUTATIVE	protein	214	71% helix, 1% strand	Q8I374
K	Subunit of proteaseome activator COMPLEX,PUTATIVE	protein	223	71% helix, 2% strand	Q8I374
L	Subunit of proteaseome activator COMPLEX,PUTATIVE	protein	233	64% helix, 4% strand	Q8I374
M	Subunit of proteaseome activator COMPLEX,PUTATIVE	protein	213	71% helix, 1% strand	Q8I374
N	Subunit of proteaseome activator COMPLEX,PUTATIVE	protein	233	65% helix, 4% strand	Q8I374

Ligands and binding sites

SO4 · Sulfate ion · ion · 60 copies · chains A, G, B, C, D, E, F, H, I, J, K, L, M, N

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	650	0.87	0.92	93	empty
2	507	0.81	0.87	63	empty
3	620	0.74	0.80	75	SO4
4	652	0.74	0.80	71	SO4
5	669	0.74	0.80	72	SO4

Interfaces

27 interfaces between chains.

H–I · 3304 Å² buried · 35 hydrogen bonds · protein-protein
K–L · 3198 Å² buried · 28 hydrogen bonds · protein-protein
C–D · 3142 Å² buried · 27 hydrogen bonds · protein-protein
M–N · 3110 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 2978 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

6DFK · Crystal structure of the 11S subunit of the Plasmodium falciparum proteasome, PA28 · the same entry in another collection · chain M against M, 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 Q8I374
Elsewhere: RCSB PDB 6DFK · PDBe 6DFK · UniProt Q8I374

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