MolNFT v1 · #114619 · protein

Crystal structure of E. COLI hpii catalase variant

5BV2 · Catalase hpii: “Crystal structure of E. COLI hpii catalase variant”. X-ray diffraction, 3 ligands (HDD, MG, SO4), 20 pockets (best druggability 0.89). MolNFT v1 #114619 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5BV2
Type: protein
Length: 2,987 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, MG, SO4
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P, R, S	Catalase hpii (EC 1.11.1.6)	protein	747	32% helix, 17% strand	P21179
Q	Catalase hpii (EC 1.11.1.6)	protein	746	32% helix, 17% strand	P21179

Ligands and binding sites

HDD · Cis-heme D hydroxychlorin gamma-spirolactone · ligand · 4 copies · chains P, S, Q, R
MG · Magnesium ion · metal · 2 copies · chains R, S
SO4 · Sulfate ion · ion · 2 copies · chains P, R, S
EDO · 1,2-ethanediol · additive · 39 copies · chains P, R, S, Q
GOL · Glycerol · additive · 11 copies · chains P, Q, R, S
PEG · Di(hydroxyethyl)ether · additive · 10 copies · chains P, S, Q, R
PGE · Triethylene glycol · additive · 3 copies · chains P, R
PG4 · Tetraethylene glycol · additive · chains R

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	501	0.89	0.96	65	empty
2	496	0.89	0.96	64	GOL
3	303	0.86	0.97	54	HDD, GOL
4	381	0.86	0.95	45	empty
5	282	0.86	0.96	48	HDD, GOL

Interfaces

6 interfaces between chains.

P–S · 7572 Å² buried · 162 hydrogen bonds · protein-protein
Q–R · 7490 Å² buried · 161 hydrogen bonds · protein-protein
P–R · 6066 Å² buried · 89 hydrogen bonds · protein-protein
Q–S · 6022 Å² buried · 89 hydrogen bonds · protein-protein
P–Q · 2298 Å² buried · 41 hydrogen bonds · protein-protein

Compared structures

5BV2 · Crystal structure of E. coli HPII catalase variant · the same entry in another collection · chain S against S, TM-score 1.00
P21179 · AlphaFold monomer V2.0 prediction for catalase hpii (P21179) · a predicted model of the same protein · chain Q 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 5BV2 · PDBe 5BV2 · UniProt P21179

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