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Crystal structure of the DH/PH domains of leukemia-associated rhogef in complex with rhoa

Analyse Crystal structure of the DH/PH domains of leukemia-associated rhogef in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1X86
Type: protein
Length: 2,092 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rho guanine nucleotide exchange factor 12; Transforming protein rhoa
UniProt: Q9NZN5, P61586
Ligands: PO4
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 5 distinct chains · 54% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Rho guanine nucleotide exchange factor 12	protein	362	59% helix, 14% strand	Q9NZN5
B, D	Transforming protein rhoa	protein	180	38% helix, 18% strand	P61586
E	Rho guanine nucleotide exchange factor 12	protein	336	60% helix, 9% strand	Q9NZN5
F, H	Transforming protein rhoa	protein	179	33% helix, 22% strand	P61586
G	Rho guanine nucleotide exchange factor 12	protein	314	63% helix, 5% strand	Q9NZN5

Ligands and binding sites

PO4 · Phosphate ion · ion · 4 copies · chains B, D, F, H

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	958	0.81	0.83	85	empty
2	1157	0.79	0.81	89	empty
3	972	0.79	0.81	77	empty
4	888	0.74	0.78	78	empty
5	792	0.72	0.78	74	empty

Interfaces

8 interfaces between chains.

G–H · 1752 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1742 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1628 Å² buried · 31 hydrogen bonds · protein-protein
E–F · 1561 Å² buried · 16 hydrogen bonds · protein-protein
C–G · 548 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

1X86 · Crystal Structure of the DH/PH domains of Leukemia-associated RhoGEF in complex with RhoA · the same entry in another collection · chain H against H, TM-score 1.00
Q9NZN5 · AlphaFold monomer V2.0 prediction for rho guanine nucleotide exchange factor 12 (Q9NZN5) · a predicted model of the same protein · chain E against A, TM-score 0.98
P61586 · AlphaFold monomer V2.0 prediction for transforming protein rhoa (P61586) · a predicted model of the same protein · chain F 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 Q9NZN5
Every structure of UniProt P61586
Elsewhere: RCSB PDB 1X86 · PDBe 1X86 · UniProt Q9NZN5 · UniProt P61586

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