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Crystal structure of manganese catalase from lactobacillus plantarum

Analyse Crystal structure of manganese catalase from lactobacillus plantarum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1JKU
Type: protein
Length: 1,596 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pseudocatalase
EC: 1.11.1.6
UniProt: P60355
Ligands: MN3, CA, OH
Pockets: 12 · best druggability 0.88

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Pseudocatalase (EC 1.11.1.6)	protein	266	53% helix, 6% strand	P60355

Ligands and binding sites

MN3 · Manganese (III) ion · metal · 12 copies · chains A, B, C, D, E, F
CA · Calcium ion · metal · 6 copies · chains A, F, B, C, D, E
OH · Hydroxide ion · ion · 18 copies · chains A, B, C, D, E, F

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

Pockets

12 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1042	0.88	0.89	143	empty
2	68	0.65	0.93	28	empty
3	75	0.63	0.91	27	empty
4	239	0.62	0.81	30	empty
5	237	0.62	0.81	34	empty

Interfaces

15 interfaces between chains.

D–E · 4933 Å² buried · 95 hydrogen bonds · protein-protein
B–C · 4919 Å² buried · 102 hydrogen bonds · protein-protein
A–F · 4862 Å² buried · 99 hydrogen bonds · protein-protein
A–B · 1705 Å² buried · 31 hydrogen bonds · protein-protein
D–F · 1703 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

1JKU · Crystal Structure of Manganese Catalase from Lactobacillus plantarum · the same entry in another collection · chain C against C, TM-score 1.00
P60355 · AlphaFold monomer V2.0 prediction for manganese catalase (P60355) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P60355
Elsewhere: RCSB PDB 1JKU · PDBe 1JKU · UniProt P60355

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