Structure of PDB 7ccx Chain A

Receptor sequence

>7ccxA (length=318) Species: 9606 (Homo sapiens)

MRVIRVGTRKSQLARIQTDSVVATLKASYPGLQFEIIAMSFTKELEHALE
KNEVDLVVHSLKDLPTVLPPGFTIGAICKRENPHDAVVFHPKFVGKTLET
LPEKSVVGTSSLRRAAQLQRKFPHLEFRSIRGNLNTRLRKLDEQQEFSAI
ILATAGLQRMGWHNRVGQILHPEECMYAVGQGALGVEVRAKDQDILDLVG
VLHDPETLLRCIAERAFLRHLEGGCSVPVAVHTAMKDGQLYLTGGVWSLD
GSDSIQETMQATIHVPAQHEDGPEDDPQLVGITARNIPRGPQLAAQNLGI
SLANLLLSKGAKNILDVA

3D structure

• PDB: 7ccx Crystal structures of hydroxymethylbilane synthase complexed with a substrate analog: a single substrate-binding site for four consecutive condensation steps.
• Chain: A
• Resolution: 1.84 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): K98 D99 R149 R150 R167 R173 C261
• Catalytic site (residue number reindexed from 1): K62 D63 R113 R114 R131 R137 C225
• Enzyme Commision number: 2.5.1.61: hydroxymethylbilane synthase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	DPM	A	S96 K98 D99 S146 S147 R149 R150 R173 L188 A189 Q217 C261	S60 K62 D63 S110 S111 R113 R114 R137 L152 A153 Q181 C225

Gene Ontology

Molecular Function

• GO:0004418 hydroxymethylbilane synthase activity
• GO:0005515 protein binding
• GO:0016740 transferase activity

Biological Process

• GO:0006779 porphyrin-containing compound biosynthetic process
• GO:0006782 protoporphyrinogen IX biosynthetic process
• GO:0006783 heme biosynthetic process
• GO:0006784 heme A biosynthetic process
• GO:0006785 heme B biosynthetic process
• GO:0018160 peptidyl-pyrromethane cofactor linkage
• GO:0033014 tetrapyrrole biosynthetic process
• GO:0048034 heme O biosynthetic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:7ccx, PDBe:7ccx, PDBj:7ccx
• PDBsum: 7ccx
• PubMed: 33600566
• UniProt: P08397|HEM3_HUMAN Porphobilinogen deaminase (Gene Name=HMBS)