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Porphobilinogen deaminase from vibrio cholerae

Analyse Porphobilinogen deaminase from vibrio cholerae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5H6O
Type: protein
Length: 281 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Porphobilinogen deaminase
EC: 2.5.1.61
UniProt: A0A0H6VB38
Ligands: DPM, MG
Pockets: 2 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Porphobilinogen deaminase (EC 2.5.1.61)	protein	281	36% helix, 25% strand	A0A0H6VB38

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
MG · Magnesium ion · metal · 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	515	0.70	0.80	46	DPM, MG
2	62	0.35	0.77	13	empty

Modifications

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

Compared structures

5H6O · Porphobilinogen deaminase from Vibrio Cholerae · 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 A0A0H6VB38
Elsewhere: RCSB PDB 5H6O · PDBe 5H6O · UniProt A0A0H6VB38

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