MolNFT v2 · #225437 · protein

Rhodothermus marinus alpha-amylase RmGH13_47A CBM48-A-B-C domains

8XX9: “Rhodothermus marinus alpha-amylase RmGH13_47A CBM48-A-B-C domains”. X-ray diffraction at 1.55, 2 ligands (MN, CA), 4 pockets (best druggability 0.65). MolNFT v2 #225437 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 8XX9
Type: protein
Length: 620 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.55
Source: Rhodothermus marinus JCM 9785
Molecule: alpha-amylase
EC: 3.2.1.1
Ligands: MN, CA
Pockets: 4 · best druggability 0.65

Structure

x-ray diffraction · resolution 1.55 · 1 distinct chain · 27% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	alpha-amylase (EC 3.2.1.1)	protein	620	27% helix, 23% strand	—

Ligands and binding sites

MN · Manganese (II) ion · metal · chains A
CA · Calcium ion · metal · chains A
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A
MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	377	0.65	0.79	41	empty
2	254	0.50	0.74	27	empty
3	85	0.41	0.78	17	empty
4	106	0.36	0.74	19	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 8XX9 · PDBe 8XX9

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