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Compound II structure of micrococcus lysodeikticus catalase

Analyse Compound II structure of micrococcus lysodeikticus catalase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1GWF
Type: protein
Length: 498 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catalase
EC: 1.11.1.6
UniProt: P29422
Ligands: HEM, SO4, O
Pockets: 6 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Catalase (EC 1.11.1.6)	protein	498	31% helix, 16% strand	P29422

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · chains A
SO4 · Sulfate ion · ion · 3 copies · chains A
O · Oxygen atom · ion · chains A
ACT · Acetate ion · additive · 2 copies · chains A

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	347	0.76	0.87	41	HEM, O
2	230	0.57	0.79	32	SO4
3	248	0.51	0.76	33	empty
4	50	0.34	0.79	14	empty
5	85	0.33	0.74	19	empty

Modifications

Observed in the structure: 5 modified (nonstandard).

Compared structures

1GWF · Compound II structure of Micrococcus Lysodeikticus catalase · the same entry in another collection · chain A against A, TM-score 1.00
P29422 · AlphaFold monomer V2.0 prediction for catalase (P29422) · 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 P29422
Elsewhere: RCSB PDB 1GWF · PDBe 1GWF · UniProt P29422

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