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Crystal structure of XRN1-substrate complex

Analyse Crystal structure of XRN1-substrate complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2Y35
Type: protein + DNA
Length: 1,029 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: LD22664P; DT11 (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP)-3'
EC: 3.1.13.-
UniProt: Q9VWI1
Ligands: MG
Pockets: 12 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	LD22664P (EC 3.1.13.-)	protein	1026	39% helix, 19% strand	Q9VWI1
B	DT11 (5'-D(TPTPTPTPTPTPTPTPTPTP*TP)-3'	dna	3	—	—

Ligands and binding sites

MG · Magnesium ion · metal · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

12 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	900	0.86	0.87	77	MG
2	773	0.75	0.80	82	empty
3	1136	0.73	0.76	89	empty
4	274	0.66	0.83	34	empty
5	203	0.59	0.81	32	empty

Interfaces

1 interface between chains.

A–B · 534 Å² buried · 11 hydrogen bonds · protein-nucleic

Compared structures

2Y35 · Crystal structure of Xrn1-substrate complex · 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 Q9VWI1
Elsewhere: RCSB PDB 2Y35 · PDBe 2Y35 · UniProt Q9VWI1

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