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The crystal structure of ejc in its transition state

Analyse The crystal structure of ejc in its transition state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3EX7
Type: protein + RNA
Length: 1,386 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein mago nashi homolog; RNA-binding protein 8A; Eukaryotic initiation factor 4A-III…
EC: 3.6.1.-
UniProt: P61326, Q9Y5S9, P38919, O15234
Ligands: ADP, AF3, MG
Pockets: 17 · best druggability 0.78

Structure

x-ray diffraction · 8 distinct chains · 33% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein mago nashi homolog	protein	144	35% helix, 35% strand	P61326
B	RNA-binding protein 8A	protein	94	21% helix, 29% strand	Q9Y5S9
C, H	Eukaryotic initiation factor 4A-III (EC 3.6.1.-)	protein	392	40% helix, 17% strand	P38919
D	Protein CASC3	protein	57	14% helix, 0% strand	O15234
E	Protein mago nashi homolog	protein	142	38% helix, 33% strand	P61326
G	RNA-binding protein 8A	protein	91	22% helix, 31% strand	Q9Y5S9
I	Protein CASC3	protein	62	23% helix, 0% strand	O15234
F, J	RNA (5'-R(UPUPUPUPUPU)-3')	rna	6	—	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains C, H
AF3 · Aluminum fluoride · ligand · 2 copies · chains C, H
MG · Magnesium ion · metal · 2 copies · chains C, H

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

Pockets

17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	860	0.78	0.81	77	empty
2	789	0.78	0.82	71	empty
3	923	0.75	0.78	79	empty
4	283	0.74	0.87	42	empty
5	72	0.74	0.98	20	empty

Interfaces

16 interfaces between chains.

H–I · 2315 Å² buried · 42 hydrogen bonds · protein-protein
C–D · 2285 Å² buried · 41 hydrogen bonds · protein-protein
A–C · 1678 Å² buried · 40 hydrogen bonds · protein-protein
E–H · 1643 Å² buried · 39 hydrogen bonds · protein-protein
A–B · 1344 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

3EX7 · The crystal structure of EJC in its transition state · the same entry in another collection · chain J against J, TM-score 1.00
Q9Y5S9 · AlphaFold monomer V2.0 prediction for RNA-binding protein 8A (Q9Y5S9) · a predicted model of the same protein · chain B against A, TM-score 1.00
P38919 · AlphaFold monomer V2.0 prediction for eukaryotic initiation factor 4A-III (P38919) · a predicted model of the same protein · chain C 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 P61326
Every structure of UniProt Q9Y5S9
Every structure of UniProt P38919
Every structure of UniProt O15234
Elsewhere: RCSB PDB 3EX7 · PDBe 3EX7 · UniProt P61326 · UniProt Q9Y5S9 · UniProt P38919 · UniProt O15234

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