MolNFT v1 · #171860 · protein

Crystal structure of NRAS Q61R in complex with GTP and compound 18

6ZIZ · GTPase NRAS: “Crystal structure of NRAS Q61R in complex with GTP and compound 18”. X-ray diffraction, 3 ligands (GTP, EZZ, MG), 3 pockets (best druggability 0.67). MolNFT v1 #171860 on GenesisL1: 3D structure, binding sites and…

PDB: 6ZIZ
Type: protein
Length: 339 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTPase NRAS
UniProt: P01111
Ligands: GTP, EZZ, MG
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTPase NRAS	protein	170	39% helix, 26% strand	P01111
B	GTPase NRAS	protein	169	39% helix, 26% strand	P01111

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
EZZ · (3~{S})-3-[2-[(dimethylamino)methyl]-1~{H}-indol-3-yl]-5-oxidanyl-2,3-dihydroisoindol-1-one · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

3 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	236	0.67	0.84	38	GTP, MG
2	220	0.67	0.85	39	GTP, MG
3	210	0.50	0.76	28	EZZ

Interfaces

1 interface between chains.

A–B · 665 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6ZIZ · Crystal structure of NRAS Q61R in complex with GTP and compound 18 · the same entry in another collection · chain A against A, TM-score 1.00
P01111 · AlphaFold monomer V2.0 prediction for GTPase NRAS (P01111) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P01111
Elsewhere: RCSB PDB 6ZIZ · PDBe 6ZIZ · UniProt P01111

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