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Crystal structure of aedes aegypti nibbler ntd domain

Analyse Crystal structure of aedes aegypti nibbler ntd domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JW3
Type: protein
Length: 727 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Exonuclease mut-7 homolog
EC: 3.1.-.-
UniProt: Q179T2
Pockets: 5 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 66% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Exonuclease mut-7 homolog (EC 3.1.-.-)	protein	244	67% helix, 0% strand	Q179T2
A	Exonuclease mut-7 homolog (EC 3.1.-.-)	protein	240	69% helix, 0% strand	Q179T2
B	Exonuclease mut-7 homolog (EC 3.1.-.-)	protein	243	62% helix, 0% strand	Q179T2

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	75	0.64	0.91	21	empty
2	172	0.51	0.78	29	empty
3	175	0.45	0.74	21	empty
4	63	0.35	0.77	16	empty
5	78	0.31	0.74	17	empty

Interfaces

2 interfaces between chains.

A–B · 468 Å² buried · 1 hydrogen bond · protein-protein
C–B · 417 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 modified (engineered).

Compared structures

7JW3 · Crystal structure of Aedes aegypti Nibbler NTD domain · the same entry in another collection · chain C against C, TM-score 1.00
Q179T2 · AlphaFold monomer V2.0 prediction for exonuclease mut-7 homolog (Q179T2) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 Q179T2
Elsewhere: RCSB PDB 7JW3 · PDBe 7JW3 · UniProt Q179T2

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