Research workbench

Human erythrocyte catalse cyanide complex

Analyse Human erythrocyte catalse cyanide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1DGG
Type: protein
Length: 1,988 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catalase
EC: 1.11.1.6
UniProt: P04040
Ligands: HEM, NDP, CYN
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, 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 · 2 copies · chains A, C
CYN · Cyanide ion · ion · 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	387	0.88	0.97	50	empty
2	671	0.88	0.92	50	empty
3	421	0.87	0.96	52	empty
4	265	0.85	0.96	45	CYN, HEM
5	281	0.85	0.96	46	CYN, HEM

Interfaces

6 interfaces between chains.

A–C · 4971 Å² buried · 78 hydrogen bonds · protein-protein
B–D · 4966 Å² buried · 79 hydrogen bonds · protein-protein
A–B · 4688 Å² buried · 59 hydrogen bonds · protein-protein
C–D · 4683 Å² buried · 53 hydrogen bonds · protein-protein
A–D · 2098 Å² buried · 33 hydrogen bonds · protein-protein

Compared structures

1DGG · Human erythrocyte catalse cyanide complex · the same entry in another collection · chain D against D, TM-score 1.00
P04040 · AlphaFold monomer V2.0 prediction for catalase (P04040) · a predicted model of the same protein · chain C 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 1DGG · PDBe 1DGG · UniProt P04040

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