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Crystal structure of the viral otu domain protease from qalyub virus

Analyse Crystal structure of the viral otu domain protease from qalyub virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6DX1
Type: protein
Length: 457 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-dependent RNA polymerase
UniProt: A0A191KWB3
Pockets: 6 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	RNA-dependent RNA polymerase	protein	155	41% helix, 30% strand	A0A191KWB3
A, C	RNA-dependent RNA polymerase	protein	151	42% helix, 29% strand	A0A191KWB3

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	274	0.74	0.88	34	empty
2	58	0.35	0.78	16	empty
3	50	0.34	0.79	14	empty
4	50	0.34	0.77	12	empty
5	74	0.32	0.74	18	empty

Interfaces

3 interfaces between chains.

B–C · 439 Å² buried · 4 hydrogen bonds · protein-protein
B–A · 417 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 416 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6DX1 · Crystal structure of the viral OTU domain protease from Qalyub virus · the same entry in another collection · chain B against B, 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 A0A191KWB3
Elsewhere: RCSB PDB 6DX1 · PDBe 6DX1 · UniProt A0A191KWB3

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