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Crystal structure of human SPINDLIN3

Analyse Crystal structure of human SPINDLIN3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5A1H
Type: protein
Length: 743 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spindlin-3
UniProt: Q5JUX0
Pockets: 12 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 5% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spindlin-3	protein	193	7% helix, 47% strand	Q5JUX0
B	Spindlin-3	protein	186	3% helix, 44% strand	Q5JUX0
C	Spindlin-3	protein	186	7% helix, 43% strand	Q5JUX0
D	Spindlin-3	protein	178	4% helix, 45% strand	Q5JUX0

Pockets

12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	572	0.69	0.78	56	empty
2	469	0.65	0.77	53	empty
3	78	0.56	0.86	18	empty
4	128	0.50	0.80	22	empty
5	149	0.44	0.76	24	empty

Interfaces

4 interfaces between chains.

A–C · 638 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 604 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 465 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 29 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5A1H · Crystal structure of human Spindlin3 · the same entry in another collection · chain D against D, TM-score 1.00
Q5JUX0 · AlphaFold monomer V2.0 prediction for spindlin-3 (Q5JUX0) · a predicted model of the same protein · chain D against A, TM-score 0.97

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 Q5JUX0
Elsewhere: RCSB PDB 5A1H · PDBe 5A1H · UniProt Q5JUX0

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