MolNFT v1 · #138217 · protein

Katanin hexamer in spiral conformation

5WC0 · Meiotic spindle formation protein mei-1: “Katanin hexamer in spiral conformation”. Electron microscopy, 1 ligand (ATP), 20 pockets (best druggability 0.87). MolNFT v1 #138217 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5WC0
Type: protein
Length: 1,660 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Meiotic spindle formation protein mei-1
EC: 3.6.4.3
UniProt: P34808
Ligands: ATP
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 2 distinct chains · 44% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Meiotic spindle formation protein mei-1 (EC 3.6.4.3)	protein	275	44% helix, 5% strand	P34808
B, C, D, E, F	Meiotic spindle formation protein mei-1 (EC 3.6.4.3)	protein	277	44% helix, 6% strand	P34808

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	942	0.87	0.88	151	ATP
2	888	0.84	0.86	124	empty
3	546	0.80	0.86	78	ATP
4	346	0.79	0.89	62	empty
5	428	0.76	0.85	55	empty

Interfaces

5 interfaces between chains.

A–B · 1611 Å² buried · 17 hydrogen bonds · protein-protein
D–E · 1581 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 1550 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 1540 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 1468 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

5WC0 · katanin hexamer in spiral conformation · the same entry in another collection · chain F against F, TM-score 1.00
P34808 · AlphaFold monomer V2.0 prediction for meiotic spindle formation protein mei-1 (P34808) · a predicted model of the same protein · chain B against A, TM-score 0.91

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 P34808
Elsewhere: RCSB PDB 5WC0 · PDBe 5WC0 · UniProt P34808

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