MolNFT v1 · #17917 · protein

Crystal structure of the D181E variant of catalase hpii from E. COLI

1P81: “Crystal structure of the D181E variant of catalase hpii from E. COLI”. X-ray diffraction, 1 ligand (HDD), 20 pockets (best druggability 0.89). MolNFT v1 #17917 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1P81
Type: protein
Length: 2,908 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catalase hpii
EC: 1.11.1.6
UniProt: P21179
Ligands: HDD
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Catalase hpii (EC 1.11.1.6)	protein	727	32% helix, 18% strand	P21179

Ligands and binding sites

HDD · Cis-heme D hydroxychlorin gamma-spirolactone · ligand · 4 copies · chains A, D, B, C

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	492	0.89	0.96	55	empty
2	499	0.88	0.95	58	empty
3	393	0.86	0.95	50	empty
4	289	0.85	0.95	48	HDD
5	257	0.84	0.96	34	HDD

Interfaces

6 interfaces between chains.

A–D · 6219 Å² buried · 118 hydrogen bonds · protein-protein
B–C · 6181 Å² buried · 115 hydrogen bonds · protein-protein
B–D · 5993 Å² buried · 82 hydrogen bonds · protein-protein
A–C · 5944 Å² buried · 87 hydrogen bonds · protein-protein
A–B · 2274 Å² buried · 42 hydrogen bonds · protein-protein

Compared structures

1P81 · Crystal structure of the D181E variant of catalase HPII from E. coli · the same entry in another collection · chain D against D, TM-score 1.00
P21179 · AlphaFold monomer V2.0 prediction for catalase hpii (P21179) · 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 P21179
Elsewhere: RCSB PDB 1P81 · PDBe 1P81 · UniProt P21179

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