MolNFT v1 · #123386 · protein

The crystal structure of ius-spry domain from RANBP10

5JIA · Ran-binding protein 10: “The crystal structure of ius-spry domain from RANBP10”. X-ray diffraction, 20 pockets (best druggability 0.76). MolNFT v1 #123386 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5JIA
Type: protein
Length: 3,278 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ran-binding protein 10
UniProt: Q6VN19
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 14 distinct chains · 13% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ran-binding protein 10	protein	206	13% helix, 38% strand	Q6VN19
B	Ran-binding protein 10	protein	207	13% helix, 38% strand	Q6VN19
C	Ran-binding protein 10	protein	205	13% helix, 38% strand	Q6VN19
D	Ran-binding protein 10	protein	210	14% helix, 37% strand	Q6VN19
E	Ran-binding protein 10	protein	207	13% helix, 38% strand	Q6VN19
F	Ran-binding protein 10	protein	207	14% helix, 38% strand	Q6VN19
G, K, N	Ran-binding protein 10	protein	203	12% helix, 37% strand	Q6VN19
H	Ran-binding protein 10	protein	203	12% helix, 38% strand	Q6VN19
I	Ran-binding protein 10	protein	206	13% helix, 37% strand	Q6VN19
J	Ran-binding protein 10	protein	199	10% helix, 38% strand	Q6VN19
L	Ran-binding protein 10	protein	205	13% helix, 38% strand	Q6VN19
M	Ran-binding protein 10	protein	208	13% helix, 38% strand	Q6VN19
O	Ran-binding protein 10	protein	202	11% helix, 39% strand	Q6VN19
P	Ran-binding protein 10	protein	204	12% helix, 38% strand	Q6VN19

Ligands and binding sites

IMD · Imidazole · additive · 8 copies · chains A, M, D, O, E, G, F, H, I, J, N, P

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	863	0.76	0.80	72	empty
2	1127	0.74	0.77	81	empty
3	1058	0.74	0.77	76	empty
4	1111	0.72	0.76	100	empty
5	553	0.69	0.79	45	empty

Interfaces

29 interfaces between chains.

A–M · 572 Å² buried · 12 hydrogen bonds · protein-protein
I–J · 569 Å² buried · 9 hydrogen bonds · protein-protein
D–O · 560 Å² buried · 11 hydrogen bonds · protein-protein
A–G · 558 Å² buried · 11 hydrogen bonds · protein-protein
F–H · 542 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5JIA · The Crystal Structure Of IUS-SPRY Domain From RanBP10 · the same entry in another collection · chain J against J, 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 Q6VN19
Elsewhere: RCSB PDB 5JIA · PDBe 5JIA · UniProt Q6VN19

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