MolNFT v1 · #29542 · protein

Crystal structure of full-length 3'-exonuclease

1ZBU · 3'-5' exonuclease ERI1: “Crystal structure of full-length 3'-exonuclease”. X-ray diffraction, 2 ligands (AMP, MG), 13 pockets (best druggability 0.75). MolNFT v1 #29542 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1ZBU
Type: protein
Length: 979 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3'-5' exonuclease ERI1
EC: 3.1.-.-
UniProt: Q8IV48
Ligands: AMP, MG
Pockets: 13 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	3'-5' exonuclease ERI1 (EC 3.1.-.-)	protein	225	36% helix, 20% strand	Q8IV48
B	3'-5' exonuclease ERI1 (EC 3.1.-.-)	protein	304	38% helix, 18% strand	Q8IV48

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 8 copies · chains A, B, C, D

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

Pockets

13 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	1008	0.75	0.78	74	MG, AMP
2	568	0.72	0.80	75	empty
3	94	0.64	0.90	19	empty
4	288	0.59	0.78	29	MG, AMP
5	309	0.56	0.76	36	MG, AMP

Interfaces

3 interfaces between chains.

A–B · 837 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 608 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 159 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 34 modified (engineered).

Compared structures

1ZBU · crystal structure of full-length 3'-exonuclease · the same entry in another collection · chain D against D, TM-score 1.00
Q8IV48 · AlphaFold monomer V2.0 prediction for 3'-5' exoribonuclease 1 (Q8IV48) · a predicted model of the same protein · 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 Q8IV48
Elsewhere: RCSB PDB 1ZBU · PDBe 1ZBU · UniProt Q8IV48

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