Structure of PDB 3bvd Chain A

Receptor sequence

>3bvdA (length=550) Species: 300852 (Thermus thermophilus HB8)

EAYPEKKATLYFLVLGFLALIVGSLFGPFQALNYGNVDAYPLLKRLLPFV
QSYYQGLTLHGVLNAIVFTQLFAQAIMVYLPARELNMRPNMGLMWLSWWM
AFIGLVVAALPLLANEATVLYTFYPPLKGHWAFYLGASVFVLSTWVSIYI
VLDLWRRWKAANPGKVTPLVTYMAVVFWLMWFLASLGLVLEAVLFLLPWS
FGLVEGVDPLVARTLFWWTGHPIVYFWLLPAYAIIYTILPKQAGGRLVSD
PMARLAFLLFLLLSTPVGFHHQFADPGIDPTWKMIHSVLTLFVAVPSLMT
AFTVAASLEFAGRLRGGRGLFGWIRALPWDNPAFVAPVLGLLGFIPGGAG
GIVNASFTLDYVVHNTAWVPGHFHLQVASLVTLTAMGSLYWLLPNLTGKP
ISDAQRRLGLAVVWLWFLGMMIMAVGLHWAGLLNVPRRAYIAQVPDAYPH
AAVPMVFNVLAGIVLLVALLLFIYGLFSVLLSRERKPELAEAPLPFAEVI
SGPEDRRLVLAMDRIGFWFAVAAILVVLAYGPTLVQLFGHLNPVPGWRLW

3D structure

• PDB: 3bvd Crystallographic Studies of Xe and Kr Binding within the Large Internal Cavity of Cytochrome ba3 from Thermus thermophilus: Structural Analysis and Role of Oxygen Transport Channels in the Heme-Cu Oxidases.
• Chain: A
• Resolution: 3.37 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H72 P101 Y133 S155 T156 H233 I235 Y237 Y248 H282 H283 S309 G331 H384 F385 H386 R449 R450
• Catalytic site (residue number reindexed from 1): H60 P89 Y121 S143 T144 H221 I223 Y225 Y236 H270 H271 S297 G319 H372 F373 H374 R437 R438
• Enzyme Commision number: 7.1.1.9: cytochrome-c oxidase.

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	CU	A	H233 H282 H283	H221 H270 H271
BS02	HEM	A	G39 P40 Y46 Y65 L69 H72 N76 Y133 F385 H386 V389 A390 M435 R450 L477	G27 P28 Y34 Y53 L57 H60 N64 Y121 F373 H374 V377 A378 M423 R438 L465
BS03	HAS	A	Y133 W229 V236 Y237 W239 H282 S309 A313 A317 L353 L354 F356 G360 G363 N366 A367 D372 H376 V381 H384 F385 Q388 V389 R449	Y121 W217 V224 Y225 W227 H270 S297 A301 A305 L341 L342 F344 G348 G351 N354 A355 D360 H364 V369 H372 F373 Q376 V377 R437

Gene Ontology

Molecular Function

• GO:0004129 cytochrome-c oxidase activity
• GO:0020037 heme binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006119 oxidative phosphorylation
• GO:0009060 aerobic respiration
• GO:1902600 proton transmembrane transport

Cellular Component

• GO:0005886 plasma membrane
• GO:0016020 membrane

External links

• PDB: RCSB:3bvd, PDBe:3bvd, PDBj:3bvd
• PDBsum: 3bvd
• PubMed: 18376849
• UniProt: Q5SJ79|COX1_THET8 Cytochrome c oxidase subunit 1 (Gene Name=cbaA)