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Structure of the ran-binding domain from human RANBP3 (wild type)

Analyse Structure of the ran-binding domain from human RANBP3 (wild type) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2Y8F
Type: protein
Length: 486 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ran-binding protein 3
UniProt: Q9H6Z4
Ligands: CL
Pockets: 2 · best druggability 0.68

Structure

x-ray diffraction · 4 distinct chains · 19% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ran-binding protein 3	protein	127	15% helix, 53% strand	Q9H6Z4
B	Ran-binding protein 3	protein	112	21% helix, 54% strand	Q9H6Z4
C	Ran-binding protein 3	protein	114	17% helix, 56% strand	Q9H6Z4
D	Ran-binding protein 3	protein	133	24% helix, 48% strand	Q9H6Z4

Ligands and binding sites

CL · Chloride ion · ion · chains A
GOL · Glycerol · additive · 6 copies · chains A, D, C

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

Pockets

2 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	1152	0.68	0.73	100	GOL
2	126	0.53	0.81	21	empty

Interfaces

5 interfaces between chains.

A–D · 992 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 654 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 300 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 200 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 79 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2Y8F · Structure of the Ran-binding domain from human RanBP3 (wild type) · the same entry in another collection · chain D against D, TM-score 1.00
Q9H6Z4 · AlphaFold monomer V2.0 prediction for ran-binding protein 3 (Q9H6Z4) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q9H6Z4
Elsewhere: RCSB PDB 2Y8F · PDBe 2Y8F · UniProt Q9H6Z4

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