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Crystal structure of NADPH depleted bovine live catalase complexed with cyanide

Analyse Crystal structure of NADPH depleted bovine live catalase complexed with cyanide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1TH3
Type: protein
Length: 1,996 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catalase
EC: 1.11.1.6
UniProt: P00432
Ligands: HEM, CYN
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Catalase (EC 1.11.1.6)	protein	499	33% helix, 18% strand	P00432

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, D, B, C
CYN · Cyanide ion · ion · 2 copies · chains A, 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	673	0.87	0.92	50	empty
2	1074	0.87	0.88	119	HEM
3	289	0.85	0.96	43	CYN, HEM
4	306	0.85	0.95	46	CYN, HEM
5	263	0.85	0.96	43	HEM

Interfaces

6 interfaces between chains.

B–C · 4890 Å² buried · 82 hydrogen bonds · protein-protein
A–D · 4862 Å² buried · 79 hydrogen bonds · protein-protein
A–C · 4786 Å² buried · 56 hydrogen bonds · protein-protein
B–D · 4718 Å² buried · 52 hydrogen bonds · protein-protein
A–B · 2191 Å² buried · 36 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 cofactor (heme attachment).

Compared structures

1TH3 · Crystal structure of NADPH depleted bovine live catalase complexed with cyanide · 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 1TH3 · PDBe 1TH3 · UniProt P00432

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