MolNFT v1 · #120688 · protein

MMI1 yth domain

5H8A · Yth domain-containing protein MMI1: “MMI1 yth domain”. X-ray diffraction, 7 pockets (best druggability 0.76). MolNFT v1 #120688 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5H8A
Type: protein
Length: 687 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yth domain-containing protein MMI1
UniProt: O74958
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 30% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Yth domain-containing protein MMI1	protein	170	32% helix, 32% strand	O74958
B	Yth domain-containing protein MMI1	protein	172	30% helix, 31% strand	O74958
C	Yth domain-containing protein MMI1	protein	174	30% helix, 31% strand	O74958
D	Yth domain-containing protein MMI1	protein	171	30% helix, 31% strand	O74958

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	981	0.76	0.79	107	empty
2	276	0.69	0.85	48	empty
3	228	0.55	0.78	27	empty
4	129	0.40	0.75	23	empty
5	65	0.37	0.78	14	empty

Interfaces

4 interfaces between chains.

C–D · 927 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 905 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 399 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 184 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5H8A · Mmi1 YTH domain · the same entry in another collection · chain D against D, 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 0.99

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 O74958
Elsewhere: RCSB PDB 5H8A · PDBe 5H8A · UniProt O74958

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