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The NADPH binding site on beef liver catalase

Analyse The NADPH binding site on beef liver catalase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7CAT
Type: protein
Length: 996 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catalase
EC: 1.11.1.6
UniProt: P00432
Ligands: HEM, NDP
Pockets: 13 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Catalase (EC 1.11.1.6)	protein	498	33% helix, 16% strand	P00432

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B

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

Pockets

13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	280	0.85	0.95	40	HEM
2	282	0.84	0.95	41	HEM
3	1037	0.81	0.82	78	empty
4	837	0.77	0.81	74	empty
5	272	0.65	0.82	40	NDP

Interfaces

1 interface between chains.

A–B · 4871 Å² buried · 73 hydrogen bonds · protein-protein

Compared structures

7CAT · The NADPH binding site on beef liver catalase · the same entry in another collection · chain A against A, 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 7CAT · PDBe 7CAT · UniProt P00432

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