MolNFT v1 · #65683 · protein

N-terminal domain of the proteasome-activating nucleotidase of methanocaldococcus jannaschii

3H43: “N-terminal domain of the proteasome-activating nucleotidase of methanocaldococcus jannaschii”. X-ray diffraction, 6 pockets (best druggability 0.73). MolNFT v1 #65683 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3H43
Type: protein
Length: 922 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proteasome-activating nucleotidase
UniProt: Q58576
Pockets: 6 · best druggability 0.73

Structure

x-ray diffraction · 5 distinct chains · 20% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, E, F, G, J	Proteasome-activating nucleotidase	protein	76	22% helix, 41% strand	Q58576
B	Proteasome-activating nucleotidase	protein	77	19% helix, 39% strand	Q58576
H	Proteasome-activating nucleotidase	protein	78	18% helix, 38% strand	Q58576
I, L	Proteasome-activating nucleotidase	protein	79	20% helix, 39% strand	Q58576
K	Proteasome-activating nucleotidase	protein	77	21% helix, 40% strand	Q58576

Pockets

6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	879	0.73	0.77	71	empty
2	239	0.73	0.88	34	empty
3	98	0.71	0.94	25	empty
4	576	0.69	0.78	43	empty
5	668	0.67	0.76	46	empty

Interfaces

24 interfaces between chains.

K–L · 1132 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1114 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 1101 Å² buried · 16 hydrogen bonds · protein-protein
I–J · 1088 Å² buried · 20 hydrogen bonds · protein-protein
G–H · 1061 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 23 modified (engineered).

Compared structures

3H43 · N-terminal domain of the proteasome-activating nucleotidase of Methanocaldococcus… · the same entry in another collection · chain L against L, 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 Q58576
Elsewhere: RCSB PDB 3H43 · PDBe 3H43 · UniProt Q58576

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