Research workbench

Catalase structure determined by eefd (dataset 2)

Analyse Catalase structure determined by eefd (dataset 2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6JNU
Type: protein
Length: 1,996 residues
Chains: 4
Method: electron crystallography
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catalase
EC: 1.11.1.6
UniProt: P00432
Ligands: HEM, NDP
Pockets: 20 · best druggability 0.88

Structure

electron crystallography · 1 distinct chain · 33% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Catalase (EC 1.11.1.6)	protein	499	33% helix, 19% strand	P00432

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, D, B, C
NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 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, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	441	0.88	0.96	53	empty
2	698	0.88	0.92	51	empty
3	412	0.87	0.96	51	empty
4	660	0.87	0.91	116	empty
5	437	0.86	0.94	101	empty

Interfaces

6 interfaces between chains.

B–C · 4968 Å² buried · 73 hydrogen bonds · protein-protein
A–D · 4964 Å² buried · 64 hydrogen bonds · protein-protein
B–D · 4664 Å² buried · 50 hydrogen bonds · protein-protein
A–C · 4565 Å² buried · 43 hydrogen bonds · protein-protein
C–D · 2089 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

6JNU · Catalase structure determined by eEFD (dataset 2) · the same entry in another collection · chain D against D, TM-score 1.00
P00432 · AlphaFold monomer V2.0 prediction for catalase (P00432) · 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 P00432
Elsewhere: RCSB PDB 6JNU · PDBe 6JNU · UniProt P00432

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