MolNFT v1 · #68089 · protein

Catalase solved at 3.2 ångström resolution by microed

3J7B: “Catalase solved at 3.2 ångström resolution by microed”. Electron crystallography, 2 ligands (HEM, NDP), 20 pockets (best druggability 0.88). MolNFT v1 #68089 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3J7B
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 · 32% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Catalase (EC 1.11.1.6)	protein	499	32% 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	606	0.88	0.94	52	empty
2	334	0.87	0.97	47	empty
3	294	0.86	0.96	39	HEM
4	285	0.85	0.96	43	HEM
5	269	0.85	0.96	38	HEM

Interfaces

6 interfaces between chains.

A–D · 4984 Å² buried · 80 hydrogen bonds · protein-protein
B–C · 4948 Å² buried · 73 hydrogen bonds · protein-protein
B–D · 4837 Å² buried · 55 hydrogen bonds · protein-protein
A–C · 4783 Å² buried · 52 hydrogen bonds · protein-protein
A–B · 2194 Å² buried · 33 hydrogen bonds · protein-protein

Compared structures

3J7B · Catalase solved at 3.2 Angstrom resolution by MicroED · 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 B 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 3J7B · PDBe 3J7B · UniProt P00432

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