MolNFT v1 · #189375 · protein

2.29 a structure of the human catalase

7VD9: “2.29 a structure of the human catalase”. Electron microscopy, 2 ligands (HEM, NDP), 20 pockets (best druggability 0.87). MolNFT v1 #189375 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7VD9
Type: protein
Length: 1,991 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catalase
EC: 1.11.1.6
UniProt: P04040
Ligands: HEM, NDP
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 2 distinct chains · 34% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Catalase (EC 1.11.1.6)	protein	498	35% helix, 18% strand	P04040
D	Catalase (EC 1.11.1.6)	protein	497	34% helix, 19% strand	P04040

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, C, B, D
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	770	0.87	0.91	51	empty
2	258	0.85	0.96	45	HEM
3	262	0.85	0.96	38	HEM
4	248	0.84	0.96	37	HEM
5	256	0.84	0.95	37	HEM

Interfaces

6 interfaces between chains.

A–C · 5001 Å² buried · 54 hydrogen bonds · protein-protein
B–D · 4982 Å² buried · 66 hydrogen bonds · protein-protein
A–D · 4746 Å² buried · 64 hydrogen bonds · protein-protein
B–C · 4710 Å² buried · 61 hydrogen bonds · protein-protein
C–D · 2113 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

7VD9 · 2.29 A structure of the human catalase · the same entry in another collection · chain C against C, TM-score 1.00
P04040 · AlphaFold monomer V2.0 prediction for catalase (P04040) · a predicted model of the same protein · chain D 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 P04040
Elsewhere: RCSB PDB 7VD9 · PDBe 7VD9 · UniProt P04040

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