MolNFT v1 · #129795 · protein

Bacillus megaterium porphobilinogen deaminase D82E mutant

5OV5: “Bacillus megaterium porphobilinogen deaminase D82E mutant”. X-ray diffraction, 1 ligand (DPM), 2 pockets (best druggability 0.72). MolNFT v1 #129795 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5OV5
Type: protein
Length: 290 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Porphobilinogen deaminase
EC: 2.5.1.61
UniProt: Q8GCA8
Ligands: DPM
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Porphobilinogen deaminase (EC 2.5.1.61)	protein	290	38% helix, 24% strand	Q8GCA8

Ligands and binding sites

DPM · 3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	447	0.72	0.82	54	DPM
2	138	0.42	0.75	19	empty

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

5OV5 · Bacillus megaterium porphobilinogen deaminase D82E mutant · the same entry in another collection · 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 Q8GCA8
Elsewhere: RCSB PDB 5OV5 · PDBe 5OV5 · UniProt Q8GCA8

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