MolNFT v1 · #163282 · protein

Structure of deubiquitinase for pr-ubiquitination 1 -DUP1

6RYB · Septation initiation protein: “Structure of deubiquitinase for pr-ubiquitination 1 -DUP1”. X-ray diffraction, 11 pockets (best druggability 0.73). MolNFT v1 #163282 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6RYB
Type: protein
Length: 933 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Septation initiation protein
Pockets: 11 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 55% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Septation initiation protein	protein	309	55% helix, 4% strand	—
B	Septation initiation protein	protein	312	53% helix, 3% strand	—
C	Septation initiation protein	protein	312	56% helix, 5% strand	—

Pockets

11 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	943	0.73	0.77	90	empty
2	427	0.70	0.81	49	empty
3	238	0.58	0.79	39	empty
4	272	0.57	0.78	33	empty
5	62	0.52	0.86	16	empty

Interfaces

3 interfaces between chains.

B–C · 854 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 639 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 400 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6RYB · Structure of deubiquitinase for PR-ubiquitination 1 -Dup1 · 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
Elsewhere: RCSB PDB 6RYB · PDBe 6RYB

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