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Structure of the mid domain from miwi

Analyse Structure of the mid domain from miwi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4P1Z
Type: protein
Length: 496 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Piwi-like protein 1
UniProt: Q9JMB7
Pockets: 2 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 51% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Piwi-like protein 1	protein	127	50% helix, 21% strand	Q9JMB7
B	Piwi-like protein 1	protein	125	51% helix, 23% strand	Q9JMB7
C	Piwi-like protein 1	protein	126	51% helix, 22% strand	Q9JMB7
D	Piwi-like protein 1	protein	118	53% helix, 20% strand	Q9JMB7

Pockets

2 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	1060	0.74	0.77	94	empty
2	772	0.69	0.75	51	empty

Interfaces

4 interfaces between chains.

A–B · 563 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 397 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 253 Å² buried · 0 hydrogen bonds · protein-protein
C–D · 204 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

4P1Z · Structure of the MID domain from MIWI · the same entry in another collection · chain D against D, TM-score 1.00
Q9JMB7 · AlphaFold monomer V2.0 prediction for piwi-like protein 1 (Q9JMB7) · a predicted model of the same protein · chain D against A, TM-score 0.91

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 Q9JMB7
Elsewhere: RCSB PDB 4P1Z · PDBe 4P1Z · UniProt Q9JMB7

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