MolNFT v1 · #190527 · protein

Structural basis for GEMIN5 decamer-mediated mRNA binding

7XDT · Gem-associated protein 5: “Structural basis for GEMIN5 decamer-mediated mRNA binding”. Electron microscopy, 20 pockets (best druggability 0.57). MolNFT v1 #190527 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7XDT
Type: protein
Length: 5,310 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gem-associated protein 5
UniProt: Q8TEQ6
Pockets: 20 · best druggability 0.57

Structure

electron microscopy · 1 distinct chain · 73% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J	Gem-associated protein 5	protein	531	73% helix, 0% strand	Q8TEQ6

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	100	0.57	0.85	19	empty
2	104	0.56	0.84	19	empty
3	101	0.56	0.84	19	empty
4	99	0.54	0.84	18	empty
5	102	0.52	0.82	18	empty

Interfaces

20 interfaces between chains.

C–D · 3273 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 3261 Å² buried · 22 hydrogen bonds · protein-protein
I–J · 3261 Å² buried · 22 hydrogen bonds · protein-protein
G–H · 3258 Å² buried · 22 hydrogen bonds · protein-protein
E–F · 3257 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

7XDT · Structural basis for Gemin5 decamer-mediated mRNA binding · the same entry in another collection · chain J against J, TM-score 1.00
Q8TEQ6 · AlphaFold monomer V2.0 prediction for gem-associated protein 5 (Q8TEQ6) · a predicted model of the same protein · chain G against A, TM-score 0.93

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 Q8TEQ6
Elsewhere: RCSB PDB 7XDT · PDBe 7XDT · UniProt Q8TEQ6

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