MolNFT v1 · #60621 · protein

Crystal structure of pdzrhogef rgrgs domain in a complex with galpha- 13 bound to GDP

3CX6 · Guanine nucleotide-binding protein alpha-13 subunit: “Crystal structure of pdzrhogef rgrgs domain in a complex with galpha- 13 bound to GDP”. X-ray diffraction, 2 ligands (GDP, MG), 5 pockets (best druggability 0.77). MolNFT v1…

PDB: 3CX6
Type: protein
Length: 505 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanine nucleotide-binding protein alpha-13 subunit; Rho guanine nucleotide exchange…
UniProt: P27601, Q9ES67
Ligands: GDP, MG
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 57% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanine nucleotide-binding protein alpha-13 subunit	protein	320	50% helix, 13% strand	P27601
B	Rho guanine nucleotide exchange factor 11	protein	185	68% helix, 0% strand	Q9ES67

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · chains A
MG · Magnesium ion · metal · 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	587	0.77	0.83	74	MG, GDP
2	114	0.60	0.85	17	empty
3	145	0.46	0.77	23	empty
4	72	0.33	0.76	13	empty
5	74	0.30	0.73	18	empty

Interfaces

1 interface between chains.

A–B · 1336 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

3CX6 · Crystal Structure of PDZRhoGEF rgRGS Domain in a Complex with Galpha-13 Bound to GDP · the same entry in another collection · chain A against A, TM-score 1.00
P27601 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein subunit alpha-13… · a predicted model of the same protein · chain A against A, TM-score 0.99
Q9ES67 · AlphaFold monomer V2.0 prediction for rho guanine nucleotide exchange factor 11 (Q9ES67) · a predicted model of the same protein · chain B 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 P27601
Every structure of UniProt Q9ES67
Elsewhere: RCSB PDB 3CX6 · PDBe 3CX6 · UniProt P27601 · UniProt Q9ES67

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