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Crystal structure of the C-terminal tail of SARS-cov-2 ORF6 complex with human nucleoporin pair RAE1-NUP98

Analyse Crystal structure of the C-terminal tail of SARS-cov-2 ORF6 complex with human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7VPH
Type: protein
Length: 1,578 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MRNA export factor; Isoform 3 of nuclear pore complex protein NUP98-NUP96; ORF6 protein
EC: 3.4.21.-
UniProt: P78406, P52948, P0DTC6
Pockets: 19 · best druggability 0.82

Structure

x-ray diffraction · 10 distinct chains · 6% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MRNA export factor	protein	339	4% helix, 51% strand	P78406
B	Isoform 3 of nuclear pore complex protein NUP98-NUP96 (EC 3.4.21.-)	protein	51	27% helix, 22% strand	P52948
C	MRNA export factor	protein	337	3% helix, 50% strand	P78406
D	Isoform 3 of nuclear pore complex protein NUP98-NUP96 (EC 3.4.21.-)	protein	44	32% helix, 11% strand	P52948
E	MRNA export factor	protein	336	4% helix, 50% strand	P78406
F	Isoform 3 of nuclear pore complex protein NUP98-NUP96 (EC 3.4.21.-)	protein	54	24% helix, 24% strand	P52948
G	MRNA export factor	protein	336	2% helix, 50% strand	P78406
H	Isoform 3 of nuclear pore complex protein NUP98-NUP96 (EC 3.4.21.-)	protein	46	30% helix, 9% strand	P52948
I, K, X	ORF6 protein	protein	9	0% helix, 33% strand	P0DTC6
J	ORF6 protein	protein	8	0% helix, 38% strand	P0DTC6

Pockets

19 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	885	0.82	0.84	69	empty
2	871	0.82	0.84	71	empty
3	976	0.82	0.83	78	empty
4	856	0.81	0.83	65	empty
5	865	0.74	0.78	69	empty

Interfaces

19 interfaces between chains.

E–F · 1532 Å² buried · 31 hydrogen bonds · protein-protein
A–B · 1496 Å² buried · 29 hydrogen bonds · protein-protein
G–H · 1412 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 1366 Å² buried · 28 hydrogen bonds · protein-protein
C–I · 617 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

7VPH · Crystal structure of the C-terminal tail of SARS-CoV-2 Orf6 complex with human… · the same entry in another collection · chain X against X, 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 P78406
Every structure of UniProt P52948
Every structure of UniProt P0DTC6
Elsewhere: RCSB PDB 7VPH · PDBe 7VPH · UniProt P78406 · UniProt P52948 · UniProt P0DTC6

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