Research workbench

Mvm nes mutant NM15 in complex with CRM1-ran-RANBP1

Analyse Mvm nes mutant NM15 in complex with CRM1-ran-RANBP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6A3E
Type: protein
Length: 1,353 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTP-binding nuclear protein ran; Ran-specific GTPase-activating protein 1; Exportin-1…
UniProt: P62826, P41920, P30822
Ligands: GTP, MG
Pockets: 15 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 64% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTP-binding nuclear protein ran	protein	210	29% helix, 22% strand	P62826
B	Ran-specific GTPase-activating protein 1	protein	128	13% helix, 48% strand	P41920
C	Exportin-1	protein	996	79% helix, 0% strand	P30822
D	Mvm nes mutant NM15	protein	19	58% helix, 0% strand	—

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · 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

15 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	903	0.85	0.87	110	empty
2	112	0.65	0.89	29	GTP, MG
3	506	0.64	0.76	51	empty
4	452	0.61	0.75	37	empty
5	350	0.57	0.76	31	empty

Interfaces

4 interfaces between chains.

A–B · 2096 Å² buried · 33 hydrogen bonds · protein-protein
A–C · 2057 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 1043 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 179 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6A3E · MVM NES mutant Nm15 in complex with CRM1-Ran-RanBP1 · the same entry in another collection · chain A against A, TM-score 1.00
P41920 · AlphaFold monomer V2.0 prediction for ran-specific GTPase-activating protein 1 (P41920) · a predicted model of the same protein · chain B against A, TM-score 0.95

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 P62826
Every structure of UniProt P41920
Every structure of UniProt P30822
Elsewhere: RCSB PDB 6A3E · PDBe 6A3E · UniProt P62826 · UniProt P41920 · UniProt P30822

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.