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The crystal structure of the catalytic domain of amsh

Analyse The crystal structure of the catalytic domain of amsh in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3RZU
Type: protein
Length: 1,224 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Stam-binding protein
EC: 3.4.19.-
UniProt: O95630
Ligands: ZN
Pockets: 19 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 27% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Stam-binding protein (EC 3.4.19.-)	protein	176	27% helix, 35% strand	O95630
C	Stam-binding protein (EC 3.4.19.-)	protein	177	25% helix, 35% strand	O95630
E, F, G	Stam-binding protein (EC 3.4.19.-)	protein	173	27% helix, 35% strand	O95630

Ligands and binding sites

ZN · Zinc ion · metal · 14 copies · chains A, B, C, D, E, F, G

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

Pockets

19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	631	0.72	0.80	67	empty
2	572	0.71	0.80	70	empty
3	624	0.71	0.78	59	empty
4	326	0.63	0.79	31	empty
5	260	0.61	0.80	30	empty

Interfaces

11 interfaces between chains.

C–G · 786 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 760 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 746 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 742 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 734 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3RZU · The Crystal Structure of the Catalytic Domain of AMSH · the same entry in another collection · chain G against G, TM-score 1.00
O95630 · AlphaFold monomer V2.0 prediction for stam-binding protein (O95630) · 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 O95630
Elsewhere: RCSB PDB 3RZU · PDBe 3RZU · UniProt O95630

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