MolNFT v1 · #123357 · protein

Crystal structure of the ternary complex between the human rhoa, its inhibitor and the DH/PH domain of human ARHGEF11

5JHH · Rho guanine nucleotide exchange factor 11: “Crystal structure of the ternary complex between the human rhoa, its inhibitor and the DH/PH domain of human…”. X-ray diffraction, 1 ligand (RA0), 14 pockets (best druggability 0.73).…

PDB: 5JHH
Type: protein
Length: 1,070 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rho guanine nucleotide exchange factor 11; Transforming protein rhoa
UniProt: O15085, P61586
Ligands: RA0
Pockets: 14 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 54% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rho guanine nucleotide exchange factor 11	protein	356	58% helix, 14% strand	O15085
B, F	Transforming protein rhoa	protein	178	38% helix, 22% strand	P61586
E	Rho guanine nucleotide exchange factor 11	protein	358	58% helix, 16% strand	O15085

Ligands and binding sites

RA0 · 3-{3-[ethyl(quinolin-2-yl)amino]phenyl}propanoic acid · ligand · 2 copies · chains B, F
GOL · Glycerol · additive · 3 copies · chains A, B, E

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

Pockets

14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	762	0.73	0.78	63	empty
2	376	0.71	0.83	41	empty
3	683	0.71	0.78	55	GOL
4	129	0.70	0.91	25	empty
5	231	0.52	0.76	25	empty

Interfaces

3 interfaces between chains.

A–B · 1682 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 1604 Å² buried · 24 hydrogen bonds · protein-protein
A–E · 765 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5JHH · Crystal structure of the ternary complex between the human RhoA, its inhibitor and the… · the same entry in another collection · chain A against A, TM-score 1.00
P61586 · AlphaFold monomer V2.0 prediction for transforming protein rhoa (P61586) · a predicted model of the same protein · chain B against A, TM-score 0.94
O15085 · AlphaFold monomer V2.0 prediction for rho guanine nucleotide exchange factor 11 (O15085) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 O15085
Every structure of UniProt P61586
Elsewhere: RCSB PDB 5JHH · PDBe 5JHH · UniProt O15085 · UniProt P61586

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