Structure of PDB 6xd9 Chain A

Receptor sequence

>6xd9A (length=141) Species: 9606 (Homo sapiens)

VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH
GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL
LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR

3D structure

• PDB: 6xd9 VZHE-039, a novel antisickling agent that prevents erythrocyte sickling under both hypoxic and anoxic conditions.
• Chain: A
• Resolution: 2.1 Å

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	HEM	A	Y42 F43 H45 F46 H58 K61 V62 L83 L86 H87 L91 N97 F98 L101	Y42 F43 H45 F46 H58 K61 V62 L83 L86 H87 L91 N97 F98 L101
BS02	V39	A	V1 M76 P77 K127 S131 T134	V1 M76 P77 K127 S131 T134
BS03	V39	A	V1 T134	V1 T134

Gene Ontology

Molecular Function

• GO:0004601 peroxidase activity
• GO:0005344 oxygen carrier activity
• GO:0005506 iron ion binding
• GO:0005515 protein binding
• GO:0019825 oxygen binding
• GO:0020037 heme binding
• GO:0031720 haptoglobin binding
• GO:0043177 organic acid binding
• GO:0046872 metal ion binding

Biological Process

• GO:0015670 carbon dioxide transport
• GO:0015671 oxygen transport
• GO:0030185 nitric oxide transport
• GO:0042542 response to hydrogen peroxide
• GO:0042744 hydrogen peroxide catabolic process
• GO:0098869 cellular oxidant detoxification

Cellular Component

• GO:0005576 extracellular region
• GO:0005615 extracellular space
• GO:0005829 cytosol
• GO:0005833 hemoglobin complex
• GO:0016020 membrane
• GO:0031838 haptoglobin-hemoglobin complex
• GO:0070062 extracellular exosome
• GO:0071682 endocytic vesicle lumen
• GO:0072562 blood microparticle

External links

• PDB: RCSB:6xd9, PDBe:6xd9, PDBj:6xd9
• PDBsum: 6xd9
• PubMed: 33219275
• UniProt: P69905|HBA_HUMAN Hemoglobin subunit alpha (Gene Name=HBA1)