Research workbench

Oridonin in complex with CRM1#-ran-RANBP1

Analyse Oridonin 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: 6M6X
Type: protein
Length: 1,327 residues
Chains: 3
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: ODN, GTP, MG, CL
Pockets: 19 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 66% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTP-binding nuclear protein ran	protein	209	29% helix, 22% strand	P62826
B	Ran-specific GTPase-activating protein 1	protein	123	15% helix, 54% strand	P41920
C	Exportin-1	protein	995	79% helix, 0% strand	P30822

Ligands and binding sites

ODN · (1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14r, 16beta)-1,6,7,14-tetrahydroxy-7,20-epoxykauran-15-one · ligand · 3 copies · chains C
GTP · Guanosine-5'-triphosphate · ligand · chains A
MG · Magnesium ion · metal · chains A
CL · Chloride ion · ion · 4 copies · chains C
EDO · 1,2-ethanediol · additive · chains A

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

Pockets

19 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	754	0.84	0.87	94	EDO
2	96	0.64	0.90	28	MG, GTP
3	425	0.59	0.75	39	empty
4	136	0.55	0.82	25	empty
5	190	0.53	0.78	21	empty

Interfaces

3 interfaces between chains.

A–B · 2162 Å² buried · 35 hydrogen bonds · protein-protein
A–C · 2023 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 180 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 covalent (covalent ligand).

Compared structures

6M6X · Oridonin 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 0.99

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 P62826
Every structure of UniProt P41920
Every structure of UniProt P30822
Elsewhere: RCSB PDB 6M6X · PDBe 6M6X · UniProt P62826 · UniProt P41920 · UniProt P30822

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