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Structure of CSX3/CRN3 from archaeoglobus fulgidus in complex with cyclic tetra-adenylate (CA4)

Analyse Structure of CSX3/CRN3 from archaeoglobus fulgidus in complex with cyclic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YUD
Type: protein + RNA
Length: 1,018 residues
Chains: 15
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CSX3/CRN3; Cyclic tetra-adenylate (CA4)
UniProt: A0A101DCB5
Pockets: 8 · best druggability 0.61

Structure

x-ray diffraction · 9 distinct chains · 19% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CSX3/CRN3	protein	100	20% helix, 35% strand	A0A101DCB5
B	CSX3/CRN3	protein	104	17% helix, 32% strand	A0A101DCB5
C, I, J	CSX3/CRN3	protein	98	19% helix, 36% strand	A0A101DCB5
D	CSX3/CRN3	protein	99	20% helix, 35% strand	A0A101DCB5
E	CSX3/CRN3	protein	99	18% helix, 35% strand	A0A101DCB5
F	CSX3/CRN3	protein	97	20% helix, 34% strand	A0A101DCB5
G	CSX3/CRN3	protein	102	20% helix, 32% strand	A0A101DCB5
H	CSX3/CRN3	protein	103	18% helix, 34% strand	A0A101DCB5
K, M, O, P, Q	Cyclic tetra-adenylate (CA4)	rna	4	—	—

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	394	0.61	0.77	37	empty
2	455	0.61	0.76	36	empty
3	343	0.58	0.76	33	empty
4	285	0.56	0.77	33	empty
5	128	0.43	0.76	20	empty

Interfaces

29 interfaces between chains.

G–H · 1085 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1084 Å² buried · 12 hydrogen bonds · protein-protein
I–J · 1083 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 1076 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 1063 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6YUD · Structure of Csx3/Crn3 from Archaeoglobus fulgidus in complex with cyclic tetra-adenylate… · 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
Every structure of UniProt A0A101DCB5
Elsewhere: RCSB PDB 6YUD · PDBe 6YUD · UniProt A0A101DCB5

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