MolNFT v1 · #88625 · protein

AKAP13 (akap-lbc) rhogef domain in complex with rhoa

4D0N · Transforming protein rhoa: “AKAP13 (akap-lbc) rhogef domain in complex with rhoa”. X-ray diffraction, 2 ligands (GDP, SO4), 5 pockets (best druggability 0.70). MolNFT v1 #88625 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4D0N
Type: protein
Length: 550 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transforming protein rhoa; A-kinase anchor protein 13
EC: 3.6.5.2
UniProt: P61586, Q12802
Ligands: GDP, SO4
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 52% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transforming protein rhoa (EC 3.6.5.2)	protein	179	37% helix, 23% strand	P61586
B	A-kinase anchor protein 13	protein	371	59% helix, 16% strand	Q12802

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · chains A
SO4 · Sulfate ion · ion · 5 copies · chains A, B
EDO · 1,2-ethanediol · additive · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	411	0.70	0.81	46	empty
2	236	0.59	0.79	30	EDO
3	298	0.55	0.76	38	GDP
4	104	0.38	0.75	22	empty
5	57	0.29	0.75	13	empty

Interfaces

1 interface between chains.

A–B · 1508 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

4D0N · AKAP13 (AKAP-Lbc) RhoGEF domain in complex with RhoA · 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 A against A, TM-score 0.93

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 P61586
Every structure of UniProt Q12802
Elsewhere: RCSB PDB 4D0N · PDBe 4D0N · UniProt P61586 · UniProt Q12802

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