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Crystal structure of the GRB14 ra and pH domains in complex with GTP- loaded H-RAS

Analyse Crystal structure of the GRB14 ra and pH domains in complex with GTP- loaded… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4K81
Type: protein
Length: 1,660 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Growth factor receptor-bound protein 14; GTPase HRAS
UniProt: Q14449, P01112
Ligands: GTP, MG
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Growth factor receptor-bound protein 14	protein	244	23% helix, 32% strand	Q14449
B, D, F, H	GTPase HRAS	protein	171	39% helix, 28% strand	P01112

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains B, D, F, H
MG · Magnesium ion · metal · 4 copies · chains B, D, F, H
GOL · Glycerol · additive · 9 copies · chains A, B, C, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	806	0.84	0.87	75	GOL
2	643	0.83	0.88	56	empty
3	976	0.83	0.84	106	GTP, MG
4	708	0.83	0.87	76	GOL
5	645	0.83	0.87	57	GOL

Interfaces

16 interfaces between chains.

C–G · 692 Å² buried · 3 hydrogen bonds · protein-protein
A–E · 676 Å² buried · 4 hydrogen bonds · protein-protein
E–H · 618 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 607 Å² buried · 12 hydrogen bonds · protein-protein
F–G · 567 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

4K81 · Crystal structure of the Grb14 RA and PH domains in complex with GTP-loaded H-Ras · the same entry in another collection · chain H against H, TM-score 1.00
Q14449 · AlphaFold monomer V2.0 prediction for growth factor receptor-bound protein 14 (Q14449) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q14449
Every structure of UniProt P01112
Elsewhere: RCSB PDB 4K81 · PDBe 4K81 · UniProt Q14449 · UniProt P01112

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