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Apo-structure of yth domain of SPMMI1

Analyse Apo-structure of yth domain of SPMMI1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5EIP
Type: protein
Length: 268 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yth domain-containing protein MMI1
UniProt: O74958
Pockets: 4 · best druggability 0.50

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Yth domain-containing protein MMI1	protein	134	31% helix, 34% strand	O74958

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	169	0.50	0.78	26	empty
2	133	0.41	0.75	28	empty
3	70	0.41	0.80	19	empty
4	69	0.34	0.76	19	empty

Interfaces

1 interface between chains.

A–B · 533 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5EIP · apo-structure of YTH domain of SpMmi1 · the same entry in another collection · chain A against A, TM-score 1.00
O74958 · AlphaFold monomer V2.0 prediction for RNA binding exosome specificity factor MMI1 (O74958) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 O74958
Elsewhere: RCSB PDB 5EIP · PDBe 5EIP · UniProt O74958

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