MolNFT v1 · #99559 · protein

Crystal structure of potato rx-cc domain in complex with RANGAP2-wpp domain

4M70 · Rx protein: “Crystal structure of potato rx-cc domain in complex with RANGAP2-wpp domain”. X-ray diffraction, 17 pockets (best druggability 0.71). MolNFT v1 #99559 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4M70
Type: protein
Length: 927 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rx protein; Ran GTPase activating protein 2
UniProt: Q9XGF5, I7JSB1
Pockets: 17 · best druggability 0.71

Structure

x-ray diffraction · 10 distinct chains · 79% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rx protein	protein	107	89% helix, 0% strand	Q9XGF5
E	Ran GTPase activating protein 2	protein	88	68% helix, 0% strand	I7JSB1
L	Rx protein	protein	112	87% helix, 0% strand	Q9XGF5
J	Ran GTPase activating protein 2	protein	89	66% helix, 0% strand	I7JSB1
I	Rx protein	protein	108	88% helix, 0% strand	Q9XGF5
B	Ran GTPase activating protein 2	protein	91	65% helix, 0% strand	I7JSB1
H	Rx protein	protein	112	87% helix, 0% strand	Q9XGF5
Q	Rx protein	protein	108	88% helix, 0% strand	Q9XGF5
K	Ran GTPase activating protein 2	protein	56	70% helix, 0% strand	I7JSB1
R	Ran GTPase activating protein 2	protein	56	71% helix, 0% strand	I7JSB1

Pockets

17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	419	0.71	0.82	62	empty
2	448	0.70	0.81	59	empty
3	225	0.59	0.80	33	empty
4	149	0.53	0.80	31	empty
5	58	0.52	0.87	20	empty

Interfaces

14 interfaces between chains.

B–H · 1277 Å² buried · 9 hydrogen bonds · protein-protein
E–L · 1265 Å² buried · 12 hydrogen bonds · protein-protein
J–I · 1261 Å² buried · 7 hydrogen bonds · protein-protein
Q–K · 979 Å² buried · 7 hydrogen bonds · protein-protein
L–J · 753 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

4M70 · Crystal structure of potato Rx-CC domain in complex with RanGAP2-WPP domain · the same entry in another collection · chain A against A, TM-score 1.00

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 Q9XGF5
Every structure of UniProt I7JSB1
Elsewhere: RCSB PDB 4M70 · PDBe 4M70 · UniProt Q9XGF5 · UniProt I7JSB1

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