Research workbench

Structure of S.POMBE alpha-mannosidase AMS1

Analyse Structure of S.POMBE alpha-mannosidase AMS1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LZ1
Type: protein
Length: 4,304 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: AMS1
EC: 3.2.1.24
UniProt: Q9UT61
Ligands: ZN
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 1 distinct chain · 25% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	AMS1 (EC 3.2.1.24)	protein	1076	25% helix, 28% strand	Q9UT61

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B, C, D

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	848	0.88	0.91	93	empty
2	882	0.88	0.90	100	empty
3	128	0.80	0.97	27	empty
4	127	0.79	0.97	27	empty
5	131	0.79	0.97	25	empty

Interfaces

6 interfaces between chains.

B–D · 2266 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 2256 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 2198 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 2198 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1378 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

6LZ1 · Structure of S.pombe alpha-mannosidase Ams1 · the same entry in another collection · chain A against A, TM-score 1.00
Q9UT61 · AlphaFold monomer V2.0 prediction for alpha-mannosidase (Q9UT61) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q9UT61
Elsewhere: RCSB PDB 6LZ1 · PDBe 6LZ1 · UniProt Q9UT61

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.