MolNFT v1 · #67248 · protein

Crystal structure of era in complex with GDP

3IEU · GTP-binding protein era: “Crystal structure of era in complex with GDP”. X-ray diffraction, 2 ligands (GDP, SO4), 5 pockets (best druggability 0.76). MolNFT v1 #67248 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3IEU
Type: protein
Length: 586 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTP-binding protein era
UniProt: P06616
Ligands: GDP, SO4
Pockets: 5 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	GTP-binding protein era	protein	293	37% helix, 25% strand	P06616

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 13 copies · chains A, B
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	992	0.76	0.79	82	GDP
2	930	0.76	0.79	76	GDP
3	144	0.41	0.74	28	empty
4	73	0.29	0.72	15	empty
5	61	0.28	0.73	16	empty

Interfaces

1 interface between chains.

A–B · 880 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

3IEU · Crystal Structure of ERA in Complex with GDP · the same entry in another collection · chain A against A, TM-score 1.00
P06616 · AlphaFold monomer V2.0 prediction for GTPase era (P06616) · a predicted model of the same protein · chain B against A, TM-score 0.59

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 P06616
Elsewhere: RCSB PDB 3IEU · PDBe 3IEU · UniProt P06616

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