MolNFT v2 · #120869 · protein

m7G cap bound to GEMIN5-WD

5H3T · Gem-associated protein 5: “m7G cap bound to GEMIN5-WD”. X-ray diffraction at 2.571, 1 ligand (MGT), 20 pockets (best druggability 0.81). MolNFT v2 #120869 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5H3T
Type: protein
Length: 2,618 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.571
Source: Homo sapiens
Molecule: Gem-associated protein 5
UniProt: Q8TEQ6
Ligands: MGT
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · resolution 2.571 · 4 distinct chains · 4% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gem-associated protein 5	protein	652	4% helix, 50% strand	Q8TEQ6
B	Gem-associated protein 5	protein	652	5% helix, 48% strand	Q8TEQ6
C	Gem-associated protein 5	protein	657	5% helix, 48% strand	Q8TEQ6
D	Gem-associated protein 5	protein	657	4% helix, 47% strand	Q8TEQ6

Ligands and binding sites

MGT · 7N-methyl-8-hydroguanosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 2 copies · chains A, D, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	979	0.81	0.82	68	MGT
2	992	0.80	0.82	73	MGT
3	1028	0.79	0.81	68	MGT
4	1007	0.79	0.81	67	MGT
5	510	0.77	0.84	48	empty

Interfaces

5 interfaces between chains.

A–C · 476 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 393 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 282 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 102 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 22 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5H3T · M7G cap bound to GEMIN5-wd · the same entry in another collection · chain D against D, TM-score 1.00
Q8TEQ6 · AlphaFold monomer V2.0 prediction for gem-associated protein 5 (Q8TEQ6) · a predicted model of the same protein · chain B 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 Q8TEQ6
Elsewhere: RCSB PDB 5H3T · PDBe 5H3T · UniProt Q8TEQ6

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