MolNFT v1 · #54913 · protein

N-terminal head domain of danio rerio sas-6

2Y3V · Spindle assembly abnormal protein 6 homolog: “N-terminal head domain of danio rerio sas-6”. X-ray diffraction, 10 pockets (best druggability 0.73). MolNFT v1 #54913 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2Y3V
Type: protein
Length: 617 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spindle assembly abnormal protein 6 homolog
UniProt: Q7ZVT3
Pockets: 10 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 21% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spindle assembly abnormal protein 6 homolog	protein	158	23% helix, 42% strand	Q7ZVT3
B	Spindle assembly abnormal protein 6 homolog	protein	159	21% helix, 42% strand	Q7ZVT3
C	Spindle assembly abnormal protein 6 homolog	protein	146	18% helix, 49% strand	Q7ZVT3
D	Spindle assembly abnormal protein 6 homolog	protein	154	21% helix, 44% strand	Q7ZVT3

Pockets

10 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	1032	0.73	0.76	94	empty
2	572	0.63	0.75	48	empty
3	127	0.45	0.77	24	empty
4	125	0.41	0.76	26	empty
5	106	0.40	0.76	23	empty

Interfaces

5 interfaces between chains.

C–D · 396 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 312 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 219 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 146 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 123 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2Y3V · N-terminal head domain of Danio rerio SAS-6 · the same entry in another collection · chain D against D, TM-score 1.00
Q7ZVT3 · AlphaFold monomer V2.0 prediction for spindle assembly abnormal protein 6 homolog (Q7ZVT3) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q7ZVT3
Elsewhere: RCSB PDB 2Y3V · PDBe 2Y3V · UniProt Q7ZVT3

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